rs3997982

Positions:

• chr6-31376517-T-A
• chr6-31376517-T-C
• chr6-31376517-T-G

Variant summary

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

The variant allele was found at a frequency of 0.847 in 152,102 control chromosomes in the GnomAD database, including 54,701 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 0.85 (54701 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.747

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.911 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.847 AC: 128783 AN: 151984 Hom.: 54652 Cov.: 32

Gnomad AFR AF: 0.833

Gnomad AMI AF: 0.922

Gnomad AMR AF: 0.891

Gnomad ASJ AF: 0.925

Gnomad EAS AF: 0.931

Gnomad SAS AF: 0.934

Gnomad FIN AF: 0.837

Gnomad MID AF: 0.927

Gnomad NFE AF: 0.829

Gnomad OTH AF: 0.877

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

GnomAD4 genome AF: 0.847 AC: 128888 AN: 152102 Hom.: 54701 Cov.: 32 AF XY: 0.851 AC XY: 63265 AN XY: 74340

Gnomad4 AFR AF: 0.833

Gnomad4 AMR AF: 0.891

Gnomad4 ASJ AF: 0.925

Gnomad4 EAS AF: 0.931

Gnomad4 SAS AF: 0.934

Gnomad4 FIN AF: 0.837

Gnomad4 NFE AF: 0.829

Gnomad4 OTH AF: 0.879

Alfa AF: 0.826 Hom.: 6144

Bravo AF: 0.848

Asia WGS AF: 0.920 AC: 3201 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	7.8
DANN	Benign	0.71

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Other links and lift over

dbSNP: rs3997982; hg19: chr6-31344294;