rs2505956

Positions:

• chr10-26896357-A-G
• chr10-26896357-A-T

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 0.601 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

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	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

Gnomad4 AFR AF: 0.300

Gnomad4 AMR AF: 0.621

Gnomad4 ASJ AF: 0.699

Gnomad4 EAS AF: 0.709

Gnomad4 SAS AF: 0.705

Gnomad4 FIN AF: 0.642

Gnomad4 NFE AF: 0.751

Gnomad4 OTH AF: 0.644

Alfa AF: 0.726 Hom.: 76814

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2505956; hg19: chr10-27185286;