rs10175798

Variant names:

• chr2-30226728-G-A
• rs10175798

Your query was ambiguous. Multiple possible variants found:

• chr2-30226728-G-A
• chr2-30226728-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 0.513 in 151,944 control chromosomes in the GnomAD database, including 21,298 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 0.51 (21298 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.138
• Publications: 39 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.48).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.608 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: 0.513 AC: 77851 AN: 151826 Hom.: 21290 Cov.: 32

Gnomad AFR AF: 0.315

Gnomad AMI AF: 0.577

Gnomad AMR AF: 0.594

Gnomad ASJ AF: 0.627

Gnomad EAS AF: 0.354

Gnomad SAS AF: 0.472

Gnomad FIN AF: 0.573

Gnomad MID AF: 0.604

Gnomad NFE AF: 0.613

Gnomad OTH AF: 0.531

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

GnomAD4 genome AF: 0.513 AC: 77889 AN: 151944 Hom.: 21298 Cov.: 32 AF XY: 0.511 AC XY: 37951 AN XY: 74242

African (AFR) AF: 0.315 AC: 13044 AN: 41402

American (AMR) AF: 0.593 AC: 9062 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.627 AC: 2174 AN: 3468

East Asian (EAS) AF: 0.355 AC: 1834 AN: 5172

South Asian (SAS) AF: 0.473 AC: 2279 AN: 4816

European-Finnish (FIN) AF: 0.573 AC: 6028 AN: 10518

Middle Eastern (MID) AF: 0.602 AC: 177 AN: 294

European-Non Finnish (NFE) AF: 0.613 AC: 41644 AN: 67988

Other (OTH) AF: 0.533 AC: 1122 AN: 2106

Alfa AF: 0.556 Hom.: 40232

Bravo AF: 0.508

Asia WGS AF: 0.404 AC: 1408 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.48
CADD	Benign	15
DANN	Benign	0.81
PhyloP100		0.14

Splicing

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

Other links and lift over

dbSNP: rs10175798; hg19: chr2-30449594;