rs1265048

chr6-31113632-T-Cchr6-31113632-T-G

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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	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;