rs10174573

Variant names:

• chr2-192877447-C-T
• rs10174573

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 0.512 in 151,582 control chromosomes in the GnomAD database, including 20,724 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 (20724 hom., cov: 30)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0230
• Publications: 8 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.01).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.587 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: 0.512 AC: 77542 AN: 151466 Hom.: 20704 Cov.: 30

Gnomad AFR AF: 0.364

Gnomad AMI AF: 0.725

Gnomad AMR AF: 0.494

Gnomad ASJ AF: 0.559

Gnomad EAS AF: 0.434

Gnomad SAS AF: 0.482

Gnomad FIN AF: 0.611

Gnomad MID AF: 0.655

Gnomad NFE AF: 0.592

Gnomad OTH AF: 0.538

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

GnomAD4 genome AF: 0.512 AC: 77604 AN: 151582 Hom.: 20724 Cov.: 30 AF XY: 0.511 AC XY: 37816 AN XY: 74050

African (AFR) AF: 0.364 AC: 15080 AN: 41384

American (AMR) AF: 0.494 AC: 7513 AN: 15204

Ashkenazi Jewish (ASJ) AF: 0.559 AC: 1937 AN: 3464

East Asian (EAS) AF: 0.434 AC: 2209 AN: 5088

South Asian (SAS) AF: 0.481 AC: 2312 AN: 4806

European-Finnish (FIN) AF: 0.611 AC: 6449 AN: 10556

Middle Eastern (MID) AF: 0.656 AC: 193 AN: 294

European-Non Finnish (NFE) AF: 0.592 AC: 40134 AN: 67776

Other (OTH) AF: 0.532 AC: 1117 AN: 2100

Alfa AF: 0.554 Hom.: 49910

Bravo AF: 0.500

Asia WGS AF: 0.435 AC: 1516 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	1.9
DANN	Benign	0.22
PhyloP100		-0.023

Splicing

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

Other links and lift over

dbSNP: rs10174573; hg19: chr2-193742173;