rs10262524

Variant names:

• chr7-116510898-C-A
• rs10262524

Your query was ambiguous. Multiple possible variants found:

• chr7-116510898-C-A
• chr7-116510898-C-T

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 0.274 in 152,046 control chromosomes in the GnomAD database, including 6,319 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 0.27 (6319 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.236
• Publications: 6 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.83).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.365 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: 0.274 AC: 41587 AN: 151928 Hom.: 6317 Cov.: 33

Gnomad AFR AF: 0.370

Gnomad AMI AF: 0.378

Gnomad AMR AF: 0.223

Gnomad ASJ AF: 0.350

Gnomad EAS AF: 0.0108

Gnomad SAS AF: 0.200

Gnomad FIN AF: 0.137

Gnomad MID AF: 0.310

Gnomad NFE AF: 0.267

Gnomad OTH AF: 0.290

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

GnomAD4 genome AF: 0.274 AC: 41614 AN: 152046 Hom.: 6319 Cov.: 33 AF XY: 0.264 AC XY: 19605 AN XY: 74312

African (AFR) AF: 0.370 AC: 15322 AN: 41438

American (AMR) AF: 0.222 AC: 3400 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.350 AC: 1212 AN: 3464

East Asian (EAS) AF: 0.0108 AC: 56 AN: 5184

South Asian (SAS) AF: 0.200 AC: 964 AN: 4818

European-Finnish (FIN) AF: 0.137 AC: 1450 AN: 10580

Middle Eastern (MID) AF: 0.299 AC: 88 AN: 294

European-Non Finnish (NFE) AF: 0.267 AC: 18172 AN: 67960

Other (OTH) AF: 0.287 AC: 605 AN: 2110

Alfa AF: 0.230 Hom.: 1270

Bravo AF: 0.286

Asia WGS AF: 0.0980 AC: 344 AN: 3470

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	11
DANN	Benign	0.43
PhyloP100		0.24

Splicing

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

Other links and lift over

dbSNP: rs10262524; hg19: chr7-116150952;