6-31516906-G-C

Variant names:

• chr6-31516906-G-C
• rs3131631

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 0.812 in 151,100 control chromosomes in the GnomAD database, including 49,902 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 0.81 (49902 hom., cov: 28)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.334

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.873 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.812 AC: 122602 AN: 150988 Hom.: 49861 Cov.: 28

Gnomad AFR AF: 0.846

Gnomad AMI AF: 0.709

Gnomad AMR AF: 0.838

Gnomad ASJ AF: 0.907

Gnomad EAS AF: 0.895

Gnomad SAS AF: 0.849

Gnomad FIN AF: 0.827

Gnomad MID AF: 0.881

Gnomad NFE AF: 0.771

Gnomad OTH AF: 0.817

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

GnomAD4 genome AF: 0.812 AC: 122693 AN: 151100 Hom.: 49902 Cov.: 28 AF XY: 0.816 AC XY: 60195 AN XY: 73764

Gnomad4 AFR AF: 0.845

Gnomad4 AMR AF: 0.839

Gnomad4 ASJ AF: 0.907

Gnomad4 EAS AF: 0.895

Gnomad4 SAS AF: 0.850

Gnomad4 FIN AF: 0.827

Gnomad4 NFE AF: 0.771

Gnomad4 OTH AF: 0.818

Alfa AF: 0.789 Hom.: 5931

Bravo AF: 0.814

Asia WGS AF: 0.811 AC: 2819 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	0.93
DANN	Benign	0.28

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs3131631; hg19: chr6-31484683;