6-31618317-C-T

Variant names:

• chr6-31618317-C-T
• rs2736177

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 0.914 in 152,046 control chromosomes in the GnomAD database, including 63,705 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 0.91 (63705 hom., cov: 29)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.06

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.973 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: 0.914 AC: 138837 AN: 151928 Hom.: 63642 Cov.: 29

Gnomad AFR AF: 0.975

Gnomad AMI AF: 0.927

Gnomad AMR AF: 0.937

Gnomad ASJ AF: 0.967

Gnomad EAS AF: 0.995

Gnomad SAS AF: 0.974

Gnomad FIN AF: 0.875

Gnomad MID AF: 0.965

Gnomad NFE AF: 0.863

Gnomad OTH AF: 0.937

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

GnomAD4 genome AF: 0.914 AC: 138958 AN: 152046 Hom.: 63705 Cov.: 29 AF XY: 0.916 AC XY: 68031 AN XY: 74308

Gnomad4 AFR AF: 0.975

Gnomad4 AMR AF: 0.937

Gnomad4 ASJ AF: 0.967

Gnomad4 EAS AF: 0.995

Gnomad4 SAS AF: 0.974

Gnomad4 FIN AF: 0.875

Gnomad4 NFE AF: 0.863

Gnomad4 OTH AF: 0.938

Alfa AF: 0.878 Hom.: 38954

Bravo AF: 0.921

Asia WGS AF: 0.980 AC: 3408 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	12
DANN	Benign	0.62

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2736177; hg19: chr6-31586094;