chr10-13313131-T-C

Variant names:

• chr10-13313131-T-C
• rs1095368

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 0.414 in 151,894 control chromosomes in the GnomAD database, including 13,244 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 0.41 (13244 hom., cov: 30)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.317
• Publications: 8 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.55).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.457 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: 0.414 AC: 62855 AN: 151776 Hom.: 13218 Cov.: 30

Gnomad AFR AF: 0.347

Gnomad AMI AF: 0.549

Gnomad AMR AF: 0.373

Gnomad ASJ AF: 0.504

Gnomad EAS AF: 0.309

Gnomad SAS AF: 0.431

Gnomad FIN AF: 0.430

Gnomad MID AF: 0.475

Gnomad NFE AF: 0.461

Gnomad OTH AF: 0.426

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

GnomAD4 genome AF: 0.414 AC: 62931 AN: 151894 Hom.: 13244 Cov.: 30 AF XY: 0.413 AC XY: 30671 AN XY: 74204

African (AFR) AF: 0.348 AC: 14426 AN: 41444

American (AMR) AF: 0.372 AC: 5668 AN: 15226

Ashkenazi Jewish (ASJ) AF: 0.504 AC: 1749 AN: 3468

East Asian (EAS) AF: 0.309 AC: 1592 AN: 5144

South Asian (SAS) AF: 0.433 AC: 2091 AN: 4828

European-Finnish (FIN) AF: 0.430 AC: 4523 AN: 10528

Middle Eastern (MID) AF: 0.476 AC: 140 AN: 294

European-Non Finnish (NFE) AF: 0.461 AC: 31334 AN: 67946

Other (OTH) AF: 0.431 AC: 908 AN: 2106

Alfa AF: 0.438 Hom.: 21228

Bravo AF: 0.405

Asia WGS AF: 0.405 AC: 1409 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.55
CADD	Benign	4.9
DANN	Benign	0.87
PhyloP100		-0.32

Splicing

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

Other links and lift over

dbSNP: rs1095368; hg19: chr10-13355131;