6-31516906-G-C

Position:

• chr6-31516906-G-C

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/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	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;