rs10500024

Variant names:

• chr7-113329365-G-A
• rs10500024

Your query was ambiguous. Multiple possible variants found:

• chr7-113329365-G-A
• chr7-113329365-G-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 0.33 in 151,884 control chromosomes in the GnomAD database, including 8,884 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 0.33 (8884 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.271
• Publications: 2 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.604 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: 0.330 AC: 50158 AN: 151768 Hom.: 8885 Cov.: 32

Gnomad AFR AF: 0.233

Gnomad AMI AF: 0.485

Gnomad AMR AF: 0.365

Gnomad ASJ AF: 0.264

Gnomad EAS AF: 0.621

Gnomad SAS AF: 0.249

Gnomad FIN AF: 0.307

Gnomad MID AF: 0.218

Gnomad NFE AF: 0.372

Gnomad OTH AF: 0.315

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

GnomAD4 genome AF: 0.330 AC: 50161 AN: 151884 Hom.: 8884 Cov.: 32 AF XY: 0.330 AC XY: 24472 AN XY: 74262

African (AFR) AF: 0.232 AC: 9636 AN: 41464

American (AMR) AF: 0.364 AC: 5556 AN: 15248

Ashkenazi Jewish (ASJ) AF: 0.264 AC: 915 AN: 3466

East Asian (EAS) AF: 0.622 AC: 3198 AN: 5144

South Asian (SAS) AF: 0.249 AC: 1200 AN: 4820

European-Finnish (FIN) AF: 0.307 AC: 3246 AN: 10558

Middle Eastern (MID) AF: 0.221 AC: 65 AN: 294

European-Non Finnish (NFE) AF: 0.372 AC: 25248 AN: 67876

Other (OTH) AF: 0.312 AC: 657 AN: 2106

Alfa AF: 0.372 Hom.: 1840

Bravo AF: 0.332

Asia WGS AF: 0.373 AC: 1295 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	1.4
DANN	Benign	0.67
PhyloP100		-0.27

Splicing

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

Other links and lift over

dbSNP: rs10500024; hg19: chr7-112969420;