6-31352761-C-T

Variant names:

• chr6-31352761-C-T
• rs2442719

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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	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;