Genetic Variant NM_178834.5:c.40G>A (chr11-111540883-G-A) – 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_178834.5(LAYN):c.40G>A(p.Val14Met) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00984 in 1,532,362 control chromosomes in the GnomAD database, including 1,179 homozygotes. In-silico tool predicts a benign outcome for this variant. 13/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.049 ( 618 hom., cov: 33)

Exomes 𝑓: 0.0055 ( 561 hom. )

Consequence

LAYN
NM_178834.5 missense

Scores

Clinical Significance

Benign criteria provided, multiple submitters, no conflicts B:2

Conservation

PhyloP100: -0.214

Variant links:

Genes affected

LAYN (HGNC:29471): (layilin) Enables hyaluronic acid binding activity. Located in focal adhesion. [provided by Alliance of Genome Resources, Apr 2022]

LAYN 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=0.0012070537).

BP6

Variant 11-111540883-G-A is Benign according to our data. Variant chr11-111540883-G-A is described in ClinVar as [Benign]. Clinvar id is 768483.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.166 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LAYN	NM_178834.5 link	c.40G>A	p.Val14Met	missense_variant	Exon 1 of 7	ENST00000375614.7	NP_849156.1	Q6UX15-2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LAYN	ENST00000375614.7 link	c.40G>A	p.Val14Met	missense_variant	Exon 1 of 7	1	NM_178834.5	ENSP00000364764.2		Q6UX15-2

Frequencies

GnomAD3 genomes

AF:

0.0490

AC:

7462

AN:

152198

Hom.:

615

Cov.:

show subpopulations

Gnomad AFR

AF:

0.169

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.0193

Gnomad ASJ

AF:

0.00576

Gnomad EAS

AF:

0.00

Gnomad SAS

AF:

0.000621

Gnomad FIN

AF:

0.000188

Gnomad MID

AF:

0.0191

Gnomad NFE

AF:

0.00103

Gnomad OTH

AF:

0.0349

GnomAD3 exomes

AF:

0.0109

AC:

1405

AN:

128318

Hom.:

108

AF XY:

0.00840

AC XY:

589

AN XY:

70148

show subpopulations

Gnomad AFR exome

AF:

0.171

Gnomad AMR exome

AF:

0.00732

Gnomad ASJ exome

AF:

0.00623

Gnomad EAS exome

AF:

0.00

Gnomad SAS exome

AF:

0.000672

Gnomad FIN exome

AF:

0.000178

Gnomad NFE exome

AF:

0.000972

Gnomad OTH exome

AF:

0.00726

GnomAD4 exome

AF:

0.00550

AC:

7584

AN:

1380056

Hom.:

561

Cov.:

AF XY:

0.00477

AC XY:

3251

AN XY:

680954

show subpopulations

Gnomad4 AFR exome

AF:

0.177

Gnomad4 AMR exome

AF:

0.00924

Gnomad4 ASJ exome

AF:

0.00447

Gnomad4 EAS exome

AF:

0.00

Gnomad4 SAS exome

AF:

0.000481

Gnomad4 FIN exome

AF:

0.000414

Gnomad4 NFE exome

AF:

0.000706

Gnomad4 OTH exome

AF:

0.0127

GnomAD4 genome

AF:

0.0492

AC:

7490

AN:

152306

Hom.:

618

Cov.:

AF XY:

0.0477

AC XY:

3553

AN XY:

74466

show subpopulations

Gnomad4 AFR

AF:

0.169

Gnomad4 AMR

AF:

0.0192

Gnomad4 ASJ

AF:

0.00576

Gnomad4 EAS

AF:

0.00

Gnomad4 SAS

AF:

0.000414

Gnomad4 FIN

AF:

0.000188

Gnomad4 NFE

AF:

0.00103

Gnomad4 OTH

AF:

0.0346

Alfa

AF:

0.0299

Hom.:

Bravo

AF:

0.0559

TwinsUK

AF:

0.000539

AC:

ALSPAC

AF:

0.000778

AC:

ExAC

AF:

0.0101

AC:

230

Asia WGS

AF:

0.0110

AC:

AN:

3474

ClinVar

Significance: Benign

Submissions summary: Benign:2

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

not provided

Benign:2

Breakthrough Genomics, Breakthrough Genomics

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: not provided

- -

Apr 19, 2018

Labcorp Genetics (formerly Invitae), Labcorp

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

AlphaMissense

Benign

0.16

BayesDel_addAF

Benign

-0.78

BayesDel_noAF

Benign

-0.75

CADD

Benign

3.1

DANN

Benign

0.85

DEOGEN2

Benign

0.0083

.;T;T;T

Eigen

Benign

-1.5

Eigen_PC

Benign

-1.6

FATHMM_MKL

Benign

0.050

LIST_S2

Benign

0.43

T;T;T;T

MetaRNN

Benign

0.0012

T;T;T;T

MetaSVM

Benign

-0.93

MutationAssessor

Benign

1.9

L;L;.;.

PrimateAI

Uncertain

0.65

PROVEAN

Benign

-0.25

N;N;N;N

REVEL

Benign

0.024

Sift

Benign

0.14

T;T;T;T

Sift4G

Benign

0.28

T;T;T;T

Polyphen

0.0070

B;B;B;B

Vest4

0.077

MPC

0.082

ClinPred

0.0023

GERP RS

-0.90

Varity_R

0.036

gMVP

0.48

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