rs10937273

Variant names:

• chr3-186831906-G-A
• rs10937273

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 0.333 in 152,096 control chromosomes in the GnomAD database, including 9,589 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 0.33 (9589 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.113
• Publications: 35 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 = 0.419 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: 0.333 AC: 50653 AN: 151978 Hom.: 9586 Cov.: 32

Gnomad AFR AF: 0.162

Gnomad AMI AF: 0.221

Gnomad AMR AF: 0.346

Gnomad ASJ AF: 0.423

Gnomad EAS AF: 0.405

Gnomad SAS AF: 0.423

Gnomad FIN AF: 0.294

Gnomad MID AF: 0.513

Gnomad NFE AF: 0.424

Gnomad OTH AF: 0.377

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

GnomAD4 genome AF: 0.333 AC: 50675 AN: 152096 Hom.: 9589 Cov.: 32 AF XY: 0.329 AC XY: 24486 AN XY: 74356

African (AFR) AF: 0.162 AC: 6730 AN: 41486

American (AMR) AF: 0.346 AC: 5289 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.423 AC: 1467 AN: 3470

East Asian (EAS) AF: 0.405 AC: 2097 AN: 5178

South Asian (SAS) AF: 0.424 AC: 2046 AN: 4822

European-Finnish (FIN) AF: 0.294 AC: 3109 AN: 10584

Middle Eastern (MID) AF: 0.520 AC: 153 AN: 294

European-Non Finnish (NFE) AF: 0.424 AC: 28783 AN: 67958

Other (OTH) AF: 0.378 AC: 799 AN: 2112

Alfa AF: 0.394 Hom.: 41673

Bravo AF: 0.327

Asia WGS AF: 0.378 AC: 1310 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	3.1
DANN	Benign	0.39
PhyloP100		0.11

Splicing

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

Other links and lift over

dbSNP: rs10937273; hg19: chr3-186549695;