rs10930597

Variant names:

• chr2-173462117-C-T
• rs10930597

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 0.139 in 152,026 control chromosomes in the GnomAD database, including 1,847 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 0.14 (1847 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.28
• Publications: 5 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 (SAS) allele frequency at 95% confidence interval = 0.226 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: 0.139 AC: 21091 AN: 151908 Hom.: 1850 Cov.: 32

Gnomad AFR AF: 0.0381

Gnomad AMI AF: 0.225

Gnomad AMR AF: 0.119

Gnomad ASJ AF: 0.212

Gnomad EAS AF: 0.0317

Gnomad SAS AF: 0.237

Gnomad FIN AF: 0.185

Gnomad MID AF: 0.177

Gnomad NFE AF: 0.193

Gnomad OTH AF: 0.147

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

GnomAD4 genome AF: 0.139 AC: 21087 AN: 152026 Hom.: 1847 Cov.: 32 AF XY: 0.139 AC XY: 10303 AN XY: 74290

African (AFR) AF: 0.0380 AC: 1576 AN: 41480

American (AMR) AF: 0.119 AC: 1817 AN: 15266

Ashkenazi Jewish (ASJ) AF: 0.212 AC: 736 AN: 3470

East Asian (EAS) AF: 0.0318 AC: 164 AN: 5164

South Asian (SAS) AF: 0.238 AC: 1143 AN: 4812

European-Finnish (FIN) AF: 0.185 AC: 1955 AN: 10548

Middle Eastern (MID) AF: 0.173 AC: 51 AN: 294

European-Non Finnish (NFE) AF: 0.193 AC: 13130 AN: 67972

Other (OTH) AF: 0.147 AC: 310 AN: 2108

Alfa AF: 0.169 Hom.: 4710

Bravo AF: 0.125

Asia WGS AF: 0.129 AC: 450 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	1.5
DANN	Benign	0.70
PhyloP100		-1.3

Splicing

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

Other links and lift over

dbSNP: rs10930597; hg19: chr2-174326845;