7-107953544-T-C

Position:

chr7-107953544-T-C

Variant summary

Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1

The NM_002291.3(LAMB1):c.3065A>G(p.Gln1022Arg) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.637 in 1,612,288 control chromosomes in the GnomAD database, including 329,260 homozygotes. In-silico tool predicts a benign outcome for this variant. 15/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★). Another nucleotide change resulting in same amino acid change has been previously reported as Likely benignin UniProt.

Frequency

Genomes: 𝑓 0.66 ( 33752 hom., cov: 32)

Exomes 𝑓: 0.63 ( 295508 hom. )

Consequence

LAMB1
NM_002291.3 missense

Scores

Clinical Significance

Benign criteria provided, multiple submitters, no conflicts B:3

Conservation

PhyloP100: -1.13

Variant links:

Genes affected

LAMB1 (HGNC:6486): (laminin subunit beta 1) Laminins, a family of extracellular matrix glycoproteins, are the major noncollagenous constituent of basement membranes. They have been implicated in a wide variety of biological processes including cell adhesion, differentiation, migration, signaling, neurite outgrowth and metastasis. Laminins are composed of 3 non identical chains: laminin alpha, beta and gamma (formerly A, B1, and B2, respectively) and they form a cruciform structure consisting of 3 short arms, each formed by a different chain, and a long arm composed of all 3 chains. Each laminin chain is a multidomain protein encoded by a distinct gene. Several isoforms of each chain have been described. Different alpha, beta and gamma chain isomers combine to give rise to different heterotrimeric laminin isoforms which are designated by Arabic numerals in the order of their discovery, i.e. alpha1beta1gamma1 heterotrimer is laminin 1. The biological functions of the different chains and trimer molecules are largely unknown, but some of the chains have been shown to differ with respect to their tissue distribution, presumably reflecting diverse functions in vivo. This gene encodes the beta chain isoform laminin, beta 1. The beta 1 chain has 7 structurally distinct domains which it shares with other beta chain isomers. The C-terminal helical region containing domains I and II are separated by domain alpha, domains III and V contain several EGF-like repeats, and domains IV and VI have a globular conformation. Laminin, beta 1 is expressed in most tissues that produce basement membranes, and is one of the 3 chains constituting laminin 1, the first laminin isolated from Engelbreth-Holm-Swarm (EHS) tumor. A sequence in the beta 1 chain that is involved in cell attachment, chemotaxis, and binding to the laminin receptor was identified and shown to have the capacity to inhibit metastasis. [provided by RefSeq, Aug 2011]

LAMB1 links:

LAMB1 (HGNC:):

LAMB1 links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -20 ACMG points.

BP4

Computational evidence support a benign effect (MetaRNN=7.994713E-7).

BP6

Variant 7-107953544-T-C is Benign according to our data. Variant chr7-107953544-T-C is described in ClinVar as [Benign]. Clinvar id is 380837.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr7-107953544-T-C is described in Lovd as [Benign].

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.821 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LAMB1	NM_002291.3 linkuse as main transcript	c.3065A>G	p.Gln1022Arg	missense_variant	22/34	ENST00000222399.11	NP_002282.2	P07942Q8TAS6
LAMB1	XM_047420359.1 linkuse as main transcript	c.3065A>G	p.Gln1022Arg	missense_variant	22/28		XP_047276315.1
LAMB1	XM_047420360.1 linkuse as main transcript	c.3065A>G	p.Gln1022Arg	missense_variant	22/25		XP_047276316.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
LAMB1	ENST00000222399.11 linkuse as main transcript	c.3065A>G	p.Gln1022Arg	missense_variant	22/34	1	NM_002291.3	ENSP00000222399.6		P07942

Frequencies

GnomAD3 genomes

AF:

0.665

AC:

100994

AN:

151960

Hom.:

33715

Cov.:

show subpopulations

Gnomad AFR

AF:

0.708

Gnomad AMI

AF:

0.624

Gnomad AMR

AF:

0.654

Gnomad ASJ

AF:

0.686

Gnomad EAS

AF:

0.843

Gnomad SAS

AF:

0.612

Gnomad FIN

AF:

0.681

Gnomad MID

AF:

0.630

Gnomad NFE

AF:

0.628

Gnomad OTH

AF:

0.642

GnomAD3 exomes

AF:

0.647

AC:

162392

AN:

251096

Hom.:

52982

AF XY:

0.641

AC XY:

87059

AN XY:

135726

show subpopulations

Gnomad AFR exome

AF:

0.704

Gnomad AMR exome

AF:

0.625

Gnomad ASJ exome

AF:

0.668

Gnomad EAS exome

AF:

0.832

Gnomad SAS exome

AF:

0.599

Gnomad FIN exome

AF:

0.667

Gnomad NFE exome

AF:

0.623

Gnomad OTH exome

AF:

0.630

GnomAD4 exome

AF:

0.634

AC:

925847

AN:

1460210

Hom.:

295508

Cov.:

AF XY:

0.632

AC XY:

459444

AN XY:

726488

show subpopulations

Gnomad4 AFR exome

AF:

0.710

Gnomad4 AMR exome

AF:

0.632

Gnomad4 ASJ exome

AF:

0.669

Gnomad4 EAS exome

AF:

0.855

Gnomad4 SAS exome

AF:

0.595

Gnomad4 FIN exome

AF:

0.663

Gnomad4 NFE exome

AF:

0.625

Gnomad4 OTH exome

AF:

0.641

GnomAD4 genome

AF:

0.665

AC:

101087

AN:

152078

Hom.:

33752

Cov.:

AF XY:

0.667

AC XY:

49608

AN XY:

74320

show subpopulations

Gnomad4 AFR

AF:

0.709

Gnomad4 AMR

AF:

0.655

Gnomad4 ASJ

AF:

0.686

Gnomad4 EAS

AF:

0.842

Gnomad4 SAS

AF:

0.612

Gnomad4 FIN

AF:

0.681

Gnomad4 NFE

AF:

0.628

Gnomad4 OTH

AF:

0.644

Alfa

AF:

0.638

Hom.:

55057

Bravo

AF:

0.662

TwinsUK

AF:

0.640

AC:

2374

ALSPAC

AF:

0.627

AC:

2417

ESP6500AA

AF:

0.705

AC:

3105

ESP6500EA

AF:

0.625

AC:

5379

ExAC

AF:

0.645

AC:

78257

Asia WGS

AF:

0.743

AC:

2582

AN:

3478

EpiCase

AF:

0.618

EpiControl

AF:

0.623

ClinVar

Significance: Benign

Submissions summary: Benign:3

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

not provided

Benign:2

Benign, criteria provided, single submitter	not provided	Breakthrough Genomics, Breakthrough Genomics	-	- -
Benign, criteria provided, single submitter	clinical testing	Labcorp Genetics (formerly Invitae), Labcorp	Jan 31, 2024	- -

not specified

Benign:1

Benign, criteria provided, single submitter

clinical testing

GeneDx

Jan 08, 2016

This variant is considered likely benign or benign based on one or more of the following criteria: it is a conservative change, it occurs at a poorly conserved position in the protein, it is predicted to be benign by multiple in silico algorithms, and/or has population frequency not consistent with disease. -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

AlphaMissense

Benign

0.059

BayesDel_addAF

Benign

-0.74

BayesDel_noAF

Benign

-0.69

CADD

Benign

0.075

DANN

Benign

0.29

DEOGEN2

Benign

0.049

.;T

Eigen

Benign

-1.6

Eigen_PC

Benign

-1.5

FATHMM_MKL

Benign

0.11

LIST_S2

Benign

0.25

T;T

MetaRNN

Benign

8.0e-7

T;T

MetaSVM

Benign

-0.95

MutationAssessor

Benign

0.11

.;N

PrimateAI

Benign

0.25

PROVEAN

Benign

-0.53

N;N

REVEL

Benign

0.091

Sift

Benign

1.0

T;T

Sift4G

Benign

0.67

T;T

Polyphen

0.0

B;B

Vest4

0.031

MPC

0.095

ClinPred

0.0018

GERP RS

-2.0

RBP_binding_hub_radar

0.0

RBP_regulation_power_radar

1.7

Varity_R

0.074

gMVP

0.39

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.0

Details are displayed if max score is > 0.2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Submissions by phenotype

Computational scores

Splicing

Publications

LitVar

Other links and lift over