rs10499934

Variant names:

• chr7-97108264-A-G
• rs10499934

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 0.191 in 151,976 control chromosomes in the GnomAD database, including 2,938 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 0.19 (2938 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.181
• Publications: 4 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.229 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: 0.191 AC: 28958 AN: 151858 Hom.: 2935 Cov.: 32

Gnomad AFR AF: 0.142

Gnomad AMI AF: 0.298

Gnomad AMR AF: 0.127

Gnomad ASJ AF: 0.231

Gnomad EAS AF: 0.129

Gnomad SAS AF: 0.165

Gnomad FIN AF: 0.226

Gnomad MID AF: 0.228

Gnomad NFE AF: 0.232

Gnomad OTH AF: 0.211

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

GnomAD4 genome AF: 0.191 AC: 28975 AN: 151976 Hom.: 2938 Cov.: 32 AF XY: 0.188 AC XY: 13977 AN XY: 74280

African (AFR) AF: 0.142 AC: 5898 AN: 41518

American (AMR) AF: 0.127 AC: 1936 AN: 15260

Ashkenazi Jewish (ASJ) AF: 0.231 AC: 800 AN: 3468

East Asian (EAS) AF: 0.128 AC: 664 AN: 5176

South Asian (SAS) AF: 0.166 AC: 800 AN: 4826

European-Finnish (FIN) AF: 0.226 AC: 2370 AN: 10508

Middle Eastern (MID) AF: 0.211 AC: 62 AN: 294

European-Non Finnish (NFE) AF: 0.232 AC: 15722 AN: 67904

Other (OTH) AF: 0.214 AC: 451 AN: 2110

Alfa AF: 0.218 Hom.: 3721

Bravo AF: 0.181

Asia WGS AF: 0.151 AC: 525 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	4.7
DANN	Benign	0.81
PhyloP100		0.18

Splicing

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

Other links and lift over

dbSNP: rs10499934; hg19: chr7-96737576;