6-31352761-C-T

Position:

• chr6-31352761-C-T

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 0.53 in 151,878 control chromosomes in the GnomAD database, including 21,722 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 0.53 (21722 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.122

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 (SAS) allele frequency at 95% confidence interval = 0.581 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: 0.530 AC: 80361 AN: 151758 Hom.: 21710 Cov.: 31

Gnomad AFR AF: 0.486

Gnomad AMI AF: 0.678

Gnomad AMR AF: 0.554

Gnomad ASJ AF: 0.595

Gnomad EAS AF: 0.326

Gnomad SAS AF: 0.599

Gnomad FIN AF: 0.473

Gnomad MID AF: 0.631

Gnomad NFE AF: 0.563

Gnomad OTH AF: 0.559

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

GnomAD4 genome AF: 0.530 AC: 80432 AN: 151878 Hom.: 21722 Cov.: 31 AF XY: 0.528 AC XY: 39202 AN XY: 74212

Gnomad4 AFR AF: 0.487

Gnomad4 AMR AF: 0.554

Gnomad4 ASJ AF: 0.595

Gnomad4 EAS AF: 0.326

Gnomad4 SAS AF: 0.599

Gnomad4 FIN AF: 0.473

Gnomad4 NFE AF: 0.563

Gnomad4 OTH AF: 0.558

Alfa AF: 0.558 Hom.: 37038

Bravo AF: 0.534

Asia WGS AF: 0.521 AC: 1813 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	8.8
DANN	Benign	0.75

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2442719; hg19: chr6-31320538;