rs7902529

Variant names:

• chr10-2256224-T-A
• rs7902529

Your query was ambiguous. Multiple possible variants found:

• chr10-2256224-T-A
• chr10-2256224-T-C

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 0.071 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
• Publications: 3 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 = 0.27 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

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

African (AFR) AF: 0.140 AC: 5823 AN: 41552

American (AMR) AF: 0.138 AC: 2109 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.0242 AC: 84 AN: 3466

East Asian (EAS) AF: 0.282 AC: 1461 AN: 5174

South Asian (SAS) AF: 0.0705 AC: 340 AN: 4824

European-Finnish (FIN) AF: 0.00622 AC: 66 AN: 10614

Middle Eastern (MID) AF: 0.0238 AC: 7 AN: 294

European-Non Finnish (NFE) AF: 0.0116 AC: 788 AN: 68018

Other (OTH) AF: 0.0592 AC: 125 AN: 2112

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 v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	4.5
DANN	Benign	0.70
PhyloP100		1.0

Splicing

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

Other links and lift over

dbSNP: rs7902529; hg19: chr10-2298418;