Genetic Variant LAMA5:c.1417+93A>G (chr20-62345988-T-C) – ACMG Classification: Benign (-20 pts)

Variant summary

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

The NM_005560.6(LAMA5):c.1417+93A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.662 in 1,582,194 control chromosomes in the GnomAD database, including 354,759 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.56 ( 27142 hom., cov: 32)

Exomes 𝑓: 0.67 ( 327617 hom. )

Consequence

LAMA5
NM_005560.6 intron

Scores

Clinical Significance

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

Conservation

PhyloP100: -0.579

Variant links:

Genes affected

LAMA5 (HGNC:6485): (laminin subunit alpha 5) This gene encodes one of the vertebrate laminin alpha chains. 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. The protein encoded by this gene is the alpha-5 subunit of of laminin-10 (laminin-511), laminin-11 (laminin-521) and laminin-15 (laminin-523). [provided by RefSeq, Jun 2013]

LAMA5 links:

LOC124904946 (HGNC:):

LOC124904946 links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -20 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.83).

BP6

Variant 20-62345988-T-C is Benign according to our data. Variant chr20-62345988-T-C is described in ClinVar as [Benign]. Clinvar id is 1297291.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.732 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LAMA5	NM_005560.6 link	c.1417+93A>G		intron_variant	Intron 10 of 79	ENST00000252999.7	NP_005551.3	O15230-1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LAMA5	ENST00000252999.7 link	c.1417+93A>G		intron_variant	Intron 10 of 79	1	NM_005560.6	ENSP00000252999.3		O15230-1
LAMA5	ENST00000370677.4 link	n.1442+93A>G		intron_variant	Intron 10 of 11	2

Frequencies

GnomAD3 genomes

AF:

0.564

AC:

85738

AN:

151944

Hom.:

27139

Cov.:

show subpopulations

Gnomad AFR

AF:

0.249

Gnomad AMI

AF:

0.809

Gnomad AMR

AF:

0.636

Gnomad ASJ

AF:

0.720

Gnomad EAS

AF:

0.752

Gnomad SAS

AF:

0.608

Gnomad FIN

AF:

0.675

Gnomad MID

AF:

0.636

Gnomad NFE

AF:

0.693

Gnomad OTH

AF:

0.613

GnomAD4 exome

AF:

0.672

AC:

961514

AN:

1430132

Hom.:

327617

Cov.:

AF XY:

0.672

AC XY:

476871

AN XY:

709932

show subpopulations

Gnomad4 AFR exome

AF:

0.229

Gnomad4 AMR exome

AF:

0.695

Gnomad4 ASJ exome

AF:

0.704

Gnomad4 EAS exome

AF:

0.783

Gnomad4 SAS exome

AF:

0.603

Gnomad4 FIN exome

AF:

0.678

Gnomad4 NFE exome

AF:

0.686

Gnomad4 OTH exome

AF:

0.659

GnomAD4 genome

AF:

0.564

AC:

85758

AN:

152062

Hom.:

27142

Cov.:

AF XY:

0.567

AC XY:

42137

AN XY:

74320

show subpopulations

Gnomad4 AFR

AF:

0.249

Gnomad4 AMR

AF:

0.636

Gnomad4 ASJ

AF:

0.720

Gnomad4 EAS

AF:

0.752

Gnomad4 SAS

AF:

0.608

Gnomad4 FIN

AF:

0.675

Gnomad4 NFE

AF:

0.693

Gnomad4 OTH

AF:

0.617

Alfa

AF:

0.673

Hom.:

60340

Bravo

AF:

0.547

Asia WGS

AF:

0.660

AC:

2295

AN:

3478

ClinVar

Significance: Benign

Submissions summary: Benign:3

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

not provided

Benign:3

Feb 03, 2025

Labcorp Genetics (formerly Invitae), Labcorp

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

- -

May 12, 2021

GeneDx

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

This variant is associated with the following publications: (PMID: 21761138) -

Breakthrough Genomics, Breakthrough Genomics

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: not provided

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.83

CADD

Benign

1.8

DANN

Benign

0.57

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