chr3-186831906-G-A

Variant names:

• chr3-186831906-G-A
• rs10937273

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 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

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;