6-31110228-C-T

Variant names:

• chr6-31110228-C-T
• rs1265062

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 0.369 in 151,910 control chromosomes in the GnomAD database, including 10,758 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 0.37 (10758 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.180

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.82).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.438 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: 0.369 AC: 55984 AN: 151790 Hom.: 10745 Cov.: 32

Gnomad AFR AF: 0.444

Gnomad AMI AF: 0.369

Gnomad AMR AF: 0.359

Gnomad ASJ AF: 0.555

Gnomad EAS AF: 0.100

Gnomad SAS AF: 0.314

Gnomad FIN AF: 0.368

Gnomad MID AF: 0.433

Gnomad NFE AF: 0.339

Gnomad OTH AF: 0.407

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

GnomAD4 genome AF: 0.369 AC: 56028 AN: 151910 Hom.: 10758 Cov.: 32 AF XY: 0.365 AC XY: 27129 AN XY: 74226

Gnomad4 AFR AF: 0.444

Gnomad4 AMR AF: 0.359

Gnomad4 ASJ AF: 0.555

Gnomad4 EAS AF: 0.100

Gnomad4 SAS AF: 0.314

Gnomad4 FIN AF: 0.368

Gnomad4 NFE AF: 0.339

Gnomad4 OTH AF: 0.404

Alfa AF: 0.356 Hom.: 863

Bravo AF: 0.373

Asia WGS AF: 0.248 AC: 864 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	5.9
DANN	Benign	0.70

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1265062; hg19: chr6-31078005;