10-2256224-T-A

Variant names:

• chr10-2256224-T-A
• rs7902529

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 0.071 in 152,254 control chromosomes in the GnomAD database, including 806 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 0.071 (806 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.04

ACMG classification

Verdict is Benign. Variant got -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 = 0.27 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: 0.0708 AC: 10776 AN: 152136 Hom.: 802 Cov.: 33

Gnomad AFR AF: 0.140

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.137

Gnomad ASJ AF: 0.0242

Gnomad EAS AF: 0.283

Gnomad SAS AF: 0.0702

Gnomad FIN AF: 0.00622

Gnomad MID AF: 0.0222

Gnomad NFE AF: 0.0116

Gnomad OTH AF: 0.0598

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

GnomAD4 genome AF: 0.0710 AC: 10803 AN: 152254 Hom.: 806 Cov.: 33 AF XY: 0.0722 AC XY: 5378 AN XY: 74446

Gnomad4 AFR AF: 0.140

Gnomad4 AMR AF: 0.138

Gnomad4 ASJ AF: 0.0242

Gnomad4 EAS AF: 0.282

Gnomad4 SAS AF: 0.0705

Gnomad4 FIN AF: 0.00622

Gnomad4 NFE AF: 0.0116

Gnomad4 OTH AF: 0.0592

Alfa AF: 0.0441 Hom.: 57

Bravo AF: 0.0885

Asia WGS AF: 0.167 AC: 578 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	4.5
DANN	Benign	0.70

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7902529; hg19: chr10-2298418;