chr3-186831366-C-G

Variant names:

• chr3-186831366-C-G
• rs10937272

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 0.37 in 151,824 control chromosomes in the GnomAD database, including 10,905 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 0.37 (10905 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.555
• Publications: 2 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.428 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Frequencies

GnomAD3 genomes AF: 0.370 AC: 56159 AN: 151706 Hom.: 10896 Cov.: 31

Gnomad AFR AF: 0.333

Gnomad AMI AF: 0.515

Gnomad AMR AF: 0.421

Gnomad ASJ AF: 0.363

Gnomad EAS AF: 0.443

Gnomad SAS AF: 0.361

Gnomad FIN AF: 0.554

Gnomad MID AF: 0.310

Gnomad NFE AF: 0.348

Gnomad OTH AF: 0.350

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

GnomAD4 genome AF: 0.370 AC: 56204 AN: 151824 Hom.: 10905 Cov.: 31 AF XY: 0.380 AC XY: 28190 AN XY: 74176

African (AFR) AF: 0.332 AC: 13762 AN: 41392

American (AMR) AF: 0.422 AC: 6435 AN: 15250

Ashkenazi Jewish (ASJ) AF: 0.363 AC: 1256 AN: 3464

East Asian (EAS) AF: 0.443 AC: 2279 AN: 5146

South Asian (SAS) AF: 0.361 AC: 1735 AN: 4802

European-Finnish (FIN) AF: 0.554 AC: 5837 AN: 10532

Middle Eastern (MID) AF: 0.310 AC: 91 AN: 294

European-Non Finnish (NFE) AF: 0.347 AC: 23601 AN: 67924

Other (OTH) AF: 0.350 AC: 739 AN: 2110

Alfa AF: 0.370 Hom.: 1330

Bravo AF: 0.360

Asia WGS AF: 0.425 AC: 1482 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	5.0
DANN	Benign	0.81
PhyloP100		0.56

Splicing

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

Other links and lift over

dbSNP: rs10937272; hg19: chr3-186549155;