rs10937273

chr3-186831906-G-A

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 0.333 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

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	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

Gnomad4 AFR AF: 0.162

Gnomad4 AMR AF: 0.346

Gnomad4 ASJ AF: 0.423

Gnomad4 EAS AF: 0.405

Gnomad4 SAS AF: 0.424

Gnomad4 FIN AF: 0.294

Gnomad4 NFE AF: 0.424

Gnomad4 OTH AF: 0.378

Alfa AF: 0.413 Hom.: 27069

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10937273; hg19: chr3-186549695;