rs10182181

Variant names:

• chr2-24927427-A-G
• rs10182181

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The variant allele was found at a frequency of 0.56 in 152,106 control chromosomes in the GnomAD database, including 26,437 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 0.56 (26437 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.180

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.836 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: 0.560 AC: 85092 AN: 151988 Hom.: 26377 Cov.: 32

Gnomad AFR AF: 0.843

Gnomad AMI AF: 0.366

Gnomad AMR AF: 0.403

Gnomad ASJ AF: 0.406

Gnomad EAS AF: 0.434

Gnomad SAS AF: 0.478

Gnomad FIN AF: 0.403

Gnomad MID AF: 0.420

Gnomad NFE AF: 0.474

Gnomad OTH AF: 0.527

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

GnomAD4 genome AF: 0.560 AC: 85207 AN: 152106 Hom.: 26437 Cov.: 32 AF XY: 0.550 AC XY: 40874 AN XY: 74338

Gnomad4 AFR AF: 0.844

Gnomad4 AMR AF: 0.402

Gnomad4 ASJ AF: 0.406

Gnomad4 EAS AF: 0.435

Gnomad4 SAS AF: 0.480

Gnomad4 FIN AF: 0.403

Gnomad4 NFE AF: 0.474

Gnomad4 OTH AF: 0.521

Alfa AF: 0.484 Hom.: 11436

Bravo AF: 0.570

Asia WGS AF: 0.457 AC: 1589 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	4.6
DANN	Benign	0.72

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10182181; hg19: chr2-25150296;