chr6-31113632-T-C

Variant names:

• chr6-31113632-T-C
• rs1265048

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 39 publications found

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

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

African (AFR) AF: 0.295 AC: 12201 AN: 41426

American (AMR) AF: 0.442 AC: 6750 AN: 15262

Ashkenazi Jewish (ASJ) AF: 0.261 AC: 907 AN: 3470

East Asian (EAS) AF: 0.541 AC: 2798 AN: 5170

South Asian (SAS) AF: 0.357 AC: 1724 AN: 4828

European-Finnish (FIN) AF: 0.470 AC: 4955 AN: 10544

Middle Eastern (MID) AF: 0.425 AC: 125 AN: 294

European-Non Finnish (NFE) AF: 0.349 AC: 23725 AN: 67962

Other (OTH) AF: 0.371 AC: 783 AN: 2112

Alfa AF: 0.357 Hom.: 30790

Bravo AF: 0.353

Asia WGS AF: 0.452 AC: 1569 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	1.1
DANN	Benign	0.52
PhyloP100		-1.1

Splicing

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

Other links and lift over

dbSNP: rs1265048; hg19: chr6-31081409;