rs10184573

Variant names:

• chr2-199583530-G-T
• rs10184573

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 0.41 in 151,914 control chromosomes in the GnomAD database, including 13,290 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 0.41 (13290 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.250
• Publications: 11 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.54 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: 0.410 AC: 62266 AN: 151796 Hom.: 13290 Cov.: 31

Gnomad AFR AF: 0.457

Gnomad AMI AF: 0.255

Gnomad AMR AF: 0.343

Gnomad ASJ AF: 0.577

Gnomad EAS AF: 0.235

Gnomad SAS AF: 0.557

Gnomad FIN AF: 0.270

Gnomad MID AF: 0.509

Gnomad NFE AF: 0.413

Gnomad OTH AF: 0.462

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

GnomAD4 genome AF: 0.410 AC: 62287 AN: 151914 Hom.: 13290 Cov.: 31 AF XY: 0.402 AC XY: 29890 AN XY: 74262

African (AFR) AF: 0.457 AC: 18906 AN: 41410

American (AMR) AF: 0.342 AC: 5222 AN: 15268

Ashkenazi Jewish (ASJ) AF: 0.577 AC: 1997 AN: 3464

East Asian (EAS) AF: 0.235 AC: 1215 AN: 5172

South Asian (SAS) AF: 0.557 AC: 2677 AN: 4804

European-Finnish (FIN) AF: 0.270 AC: 2846 AN: 10560

Middle Eastern (MID) AF: 0.500 AC: 147 AN: 294

European-Non Finnish (NFE) AF: 0.413 AC: 28059 AN: 67918

Other (OTH) AF: 0.466 AC: 986 AN: 2114

Alfa AF: 0.420 Hom.: 12066

Bravo AF: 0.414

Asia WGS AF: 0.428 AC: 1488 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	12
DANN	Benign	0.65
PhyloP100		0.25

Splicing

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

Other links and lift over

dbSNP: rs10184573; hg19: chr2-200448253;