6-31113632-T-C

Variant names:

• chr6-31113632-T-C
• rs1265048

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 0.357 in 151,980 control chromosomes in the GnomAD database, including 9,996 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 0.36 (9996 hom., cov: 32)
• 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=-0.96).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.524 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: 0.357 AC: 54179 AN: 151862 Hom.: 9985 Cov.: 32

Gnomad AFR AF: 0.294

Gnomad AMI AF: 0.288

Gnomad AMR AF: 0.442

Gnomad ASJ AF: 0.261

Gnomad EAS AF: 0.541

Gnomad SAS AF: 0.357

Gnomad FIN AF: 0.470

Gnomad MID AF: 0.418

Gnomad NFE AF: 0.349

Gnomad OTH AF: 0.368

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

GnomAD4 genome AF: 0.357 AC: 54231 AN: 151980 Hom.: 9996 Cov.: 32 AF XY: 0.366 AC XY: 27151 AN XY: 74280

Gnomad4 AFR AF: 0.295

Gnomad4 AMR AF: 0.442

Gnomad4 ASJ AF: 0.261

Gnomad4 EAS AF: 0.541

Gnomad4 SAS AF: 0.357

Gnomad4 FIN AF: 0.470

Gnomad4 NFE AF: 0.349

Gnomad4 OTH AF: 0.371

Alfa AF: 0.344 Hom.: 823

Bravo AF: 0.353

Asia WGS AF: 0.452 AC: 1569 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	1.1
DANN	Benign	0.52

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1265048; hg19: chr6-31081409;