rs6931341

Variant names:

• chr6-112282607-G-T
• rs6931341
• ENST00000587816.2:c.-398+45691G>T

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000587816.2(ENSG00000281613):​c.-398+45691G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.436 in 151,814 control chromosomes in the GnomAD database, including 15,566 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.44 (15566 hom., cov: 31)
• Consequence: ENSG00000281613 ENST00000587816.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0610
• Publications: 7 publications found

Genes affected

ENSG00000281613 (HGNC:):

LAMA4-AS1 (HGNC:40333): (LAMA4 antisense RNA 1)

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.715 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000587816.2. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LAMA4-AS1	NR_121193.1		n.182-23722G>T		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000281613	ENST00000587816.2	TSL:5	c.-398+45691G>T		intron	N/A	ENSP00000487146.1	A0A0D9SG52
	ENSG00000281613	ENST00000585611.5	TSL:5	c.-732+45691G>T		intron	N/A	ENSP00000486440.1	A0A0D9SFB2
	ENSG00000281613	ENST00000590673.5	TSL:5	c.-351+45691G>T		intron	N/A	ENSP00000486934.1	A0A0D9SFW1

Frequencies

GnomAD3 genomes AF: 0.436 AC: 66069 AN: 151696 Hom.: 15537 Cov.: 31

Gnomad AFR AF: 0.585

Gnomad AMI AF: 0.218

Gnomad AMR AF: 0.466

Gnomad ASJ AF: 0.322

Gnomad EAS AF: 0.735

Gnomad SAS AF: 0.419

Gnomad FIN AF: 0.407

Gnomad MID AF: 0.354

Gnomad NFE AF: 0.331

Gnomad OTH AF: 0.407

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.436 AC: 66149 AN: 151814 Hom.: 15566 Cov.: 31 AF XY: 0.440 AC XY: 32612 AN XY: 74154

African (AFR) AF: 0.585 AC: 24198 AN: 41384

American (AMR) AF: 0.466 AC: 7112 AN: 15256

Ashkenazi Jewish (ASJ) AF: 0.322 AC: 1117 AN: 3466

East Asian (EAS) AF: 0.735 AC: 3780 AN: 5146

South Asian (SAS) AF: 0.419 AC: 2008 AN: 4794

European-Finnish (FIN) AF: 0.407 AC: 4287 AN: 10540

Middle Eastern (MID) AF: 0.367 AC: 108 AN: 294

European-Non Finnish (NFE) AF: 0.331 AC: 22487 AN: 67920

Other (OTH) AF: 0.406 AC: 854 AN: 2106

Alfa AF: 0.354 Hom.: 19038

Bravo AF: 0.451

Asia WGS AF: 0.577 AC: 2004 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	7.4
DANN	Benign	0.57
PhyloP100		0.061

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs6931341;

hg19: chr6-112603809;

COSMIC: COSV70932952;

COSMIC: COSV70932952;