rs6931341

Positions:

• chr6-112282607-G-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NR_121193.1(LAMA4-AS1):​n.182-23722G>T variant causes a intron, non coding transcript 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: LAMA4-AS1 NR_121193.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0610

Genes affected

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

ACMG classification

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LAMA4-AS1	NR_121193.1	n.182-23722G>T		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
LAMA4-AS1	ENST00000433684.6	n.685-23722G>T		intron_variant, non_coding_transcript_variant		2

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

Gnomad4 AFR AF: 0.585

Gnomad4 AMR AF: 0.466

Gnomad4 ASJ AF: 0.322

Gnomad4 EAS AF: 0.735

Gnomad4 SAS AF: 0.419

Gnomad4 FIN AF: 0.407

Gnomad4 NFE AF: 0.331

Gnomad4 OTH AF: 0.406

Alfa AF: 0.345 Hom.: 12835

Bravo AF: 0.451

Asia WGS AF: 0.577 AC: 2004 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	7.4
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

Other links and lift over

dbSNP: rs6931341; hg19: chr6-112603809; COSMIC: COSV70932952; COSMIC: COSV70932952;