10-79361940-T-A

Variant names:

• chr10-79361940-T-A
• rs2145998

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 0.487 in 151,256 control chromosomes in the GnomAD database, including 18,240 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 0.49 (18240 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.214
• Publications: 41 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.635 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: 0.486 AC: 73519 AN: 151138 Hom.: 18207 Cov.: 31

Gnomad AFR AF: 0.422

Gnomad AMI AF: 0.470

Gnomad AMR AF: 0.597

Gnomad ASJ AF: 0.401

Gnomad EAS AF: 0.653

Gnomad SAS AF: 0.472

Gnomad FIN AF: 0.597

Gnomad MID AF: 0.468

Gnomad NFE AF: 0.476

Gnomad OTH AF: 0.500

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

GnomAD4 genome AF: 0.487 AC: 73605 AN: 151256 Hom.: 18240 Cov.: 31 AF XY: 0.494 AC XY: 36493 AN XY: 73902

African (AFR) AF: 0.422 AC: 17356 AN: 41130

American (AMR) AF: 0.598 AC: 9107 AN: 15228

Ashkenazi Jewish (ASJ) AF: 0.401 AC: 1383 AN: 3450

East Asian (EAS) AF: 0.653 AC: 3360 AN: 5146

South Asian (SAS) AF: 0.471 AC: 2256 AN: 4786

European-Finnish (FIN) AF: 0.597 AC: 6251 AN: 10468

Middle Eastern (MID) AF: 0.469 AC: 137 AN: 292

European-Non Finnish (NFE) AF: 0.476 AC: 32271 AN: 67748

Other (OTH) AF: 0.503 AC: 1058 AN: 2102

Alfa AF: 0.480 Hom.: 2194

Bravo AF: 0.485

Asia WGS AF: 0.546 AC: 1898 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	3.2
DANN	Benign	0.66
PhyloP100		0.21

Splicing

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

Other links and lift over

dbSNP: rs2145998; hg19: chr10-81121696;