10-26896357-A-G

Variant names:

• chr10-26896357-A-G
• rs2505956

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 0.601 in 152,152 control chromosomes in the GnomAD database, including 30,293 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 0.60 (30293 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.215
• Publications: 1 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.745 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: 0.601 AC: 91426 AN: 152034 Hom.: 30294 Cov.: 32

Gnomad AFR AF: 0.300

Gnomad AMI AF: 0.666

Gnomad AMR AF: 0.622

Gnomad ASJ AF: 0.699

Gnomad EAS AF: 0.709

Gnomad SAS AF: 0.704

Gnomad FIN AF: 0.642

Gnomad MID AF: 0.672

Gnomad NFE AF: 0.751

Gnomad OTH AF: 0.641

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

GnomAD4 genome AF: 0.601 AC: 91445 AN: 152152 Hom.: 30293 Cov.: 32 AF XY: 0.599 AC XY: 44562 AN XY: 74378

African (AFR) AF: 0.300 AC: 12452 AN: 41512

American (AMR) AF: 0.621 AC: 9501 AN: 15298

Ashkenazi Jewish (ASJ) AF: 0.699 AC: 2426 AN: 3470

East Asian (EAS) AF: 0.709 AC: 3663 AN: 5170

South Asian (SAS) AF: 0.705 AC: 3393 AN: 4814

European-Finnish (FIN) AF: 0.642 AC: 6802 AN: 10588

Middle Eastern (MID) AF: 0.678 AC: 198 AN: 292

European-Non Finnish (NFE) AF: 0.751 AC: 51042 AN: 67982

Other (OTH) AF: 0.644 AC: 1361 AN: 2114

Alfa AF: 0.693 Hom.: 113270

Bravo AF: 0.588

Asia WGS AF: 0.669 AC: 2324 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	12
DANN	Benign	0.94
PhyloP100		0.21

Splicing

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

Other links and lift over

dbSNP: rs2505956; hg19: chr10-27185286;