chr6-112136269-G-A

Position:

• chr6-112136269-G-A

Variant summary

Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_Strong BP6_Very_Strong BA1

The NM_001105206.3(LAMA4):​c.3283-15C>T variant causes a splice polypyrimidine tract, intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.736 in 1,594,090 control chromosomes in the GnomAD database, including 436,102 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

• Frequency:
  • Genomes: 𝑓 0.77 (46181 hom., cov: 33)
  • Exomes 𝑓: 0.73 (389921 hom.)
• Consequence: LAMA4 NM_001105206.3 splice_polypyrimidine_tract, intron
• Clinical Significance: Benign criteria provided, multiple submitters, no conflicts B:9
• Conservation: PhyloP100: -0.472

Genes affected

LAMA4 (HGNC:6484): (laminin subunit alpha 4) 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 alpha chain isoform laminin, alpha 4. The domain structure of alpha 4 is similar to that of alpha 3, both of which resemble truncated versions of alpha 1 and alpha 2, in that approximately 1,200 residues at the N-terminus (domains IV, V and VI) have been lost. Laminin, alpha 4 contains the C-terminal G domain which distinguishes all alpha chains from the beta and gamma chains. The RNA analysis from adult and fetal tissues revealed developmental regulation of expression, however, the exact function of laminin, alpha 4 is not known. Tissue-specific utilization of alternative polyA-signal has been described in literature. Alternative splicing results in multiple transcript variants encoding distinct isoforms. [provided by RefSeq, Aug 2011]

LOC107986633 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -20 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BP6: Variant 6-112136269-G-A is Benign according to our data. Variant chr6-112136269-G-A is described in ClinVar as [Benign]. Clinvar id is 44375.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr6-112136269-G-A is described in Lovd as [Benign].
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.857 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LAMA4	NM_001105206.3	c.3283-15C>T		splice_polypyrimidine_tract_variant, intron_variant		ENST00000230538.12
LOC107986633	XR_001744299.2	n.440-19051G>A		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
LAMA4	ENST00000230538.12	c.3283-15C>T		splice_polypyrimidine_tract_variant, intron_variant		1	NM_001105206.3	A1

Frequencies

GnomAD3 genomes AF: 0.775 AC: 117793 AN: 152052 Hom.: 46118 Cov.: 33

Gnomad AFR AF: 0.865

Gnomad AMI AF: 0.729

Gnomad AMR AF: 0.812

Gnomad ASJ AF: 0.757

Gnomad EAS AF: 0.864

Gnomad SAS AF: 0.872

Gnomad FIN AF: 0.734

Gnomad MID AF: 0.677

Gnomad NFE AF: 0.706

Gnomad OTH AF: 0.765

GnomAD3 exomes AF: 0.775 AC: 193138 AN: 249240 Hom.: 75707 AF XY: 0.773 AC XY: 104198 AN XY: 134824

Gnomad AFR exome AF: 0.872

Gnomad AMR exome AF: 0.873

Gnomad ASJ exome AF: 0.765

Gnomad EAS exome AF: 0.854

Gnomad SAS exome AF: 0.863

Gnomad FIN exome AF: 0.743

Gnomad NFE exome AF: 0.702

Gnomad OTH exome AF: 0.753

GnomAD4 exome AF: 0.732 AC: 1056085 AN: 1441920 Hom.: 389921 Cov.: 28 AF XY: 0.736 AC XY: 528704 AN XY: 718520

Gnomad4 AFR exome AF: 0.867

Gnomad4 AMR exome AF: 0.866

Gnomad4 ASJ exome AF: 0.759

Gnomad4 EAS exome AF: 0.862

Gnomad4 SAS exome AF: 0.858

Gnomad4 FIN exome AF: 0.740

Gnomad4 NFE exome AF: 0.707

Gnomad4 OTH exome AF: 0.747

GnomAD4 genome AF: 0.775 AC: 117918 AN: 152170 Hom.: 46181 Cov.: 33 AF XY: 0.778 AC XY: 57880 AN XY: 74386

Gnomad4 AFR AF: 0.865

Gnomad4 AMR AF: 0.812

Gnomad4 ASJ AF: 0.757

Gnomad4 EAS AF: 0.864

Gnomad4 SAS AF: 0.871

Gnomad4 FIN AF: 0.734

Gnomad4 NFE AF: 0.706

Gnomad4 OTH AF: 0.768

Alfa AF: 0.736 Hom.: 20809

Bravo AF: 0.779

Asia WGS AF: 0.891 AC: 3095 AN: 3478

ClinVar

Significance: Benign

Submissions summary: Benign:9

Revision: criteria provided, multiple submitters, no conflicts

Submissions by phenotype

not specified Benign:5

Benign, criteria provided, single submitter	clinical testing	GeneDx	Nov 22, 2013	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. -
Benign, criteria provided, single submitter	clinical testing	PreventionGenetics, part of Exact Sciences	-	- -
Benign, no assertion criteria provided	clinical testing	Clinical Genetics, Academic Medical Center	-	- -
Benign, criteria provided, single submitter	clinical testing	Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine	Sep 16, 2011	- -
Benign, criteria provided, single submitter	clinical testing	Women's Health and Genetics/Laboratory Corporation of America, LabCorp	Apr 04, 2023	- -

Dilated cardiomyopathy 1JJ Benign:4

Benign, no assertion criteria provided	clinical testing	Diagnostic Laboratory, Department of Genetics, University Medical Center Groningen	-	- -
Benign, criteria provided, single submitter	clinical testing	Clinical Genetics DNA and cytogenetics Diagnostics Lab, Erasmus MC, Erasmus Medical Center	Sep 21, 2015	- -
Benign, criteria provided, single submitter	clinical testing	Genome-Nilou Lab	Aug 19, 2021	- -
Benign, criteria provided, single submitter	clinical testing	Labcorp Genetics (formerly Invitae), Labcorp	Feb 01, 2024	- -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	0.85
DANN	Benign	0.53

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

Other links and lift over

dbSNP: rs2032568; hg19: chr6-112457471; COSMIC: COSV57893892;