chr3-132895530-G-A

Variant names:

• chr3-132895530-G-A
• rs1869151

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 0.387 in 152,108 control chromosomes in the GnomAD database, including 12,192 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 0.39 (12192 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0260
• Publications: 5 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.459 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Frequencies

GnomAD3 genomes AF: 0.387 AC: 58786 AN: 151990 Hom.: 12187 Cov.: 32

Gnomad AFR AF: 0.271

Gnomad AMI AF: 0.375

Gnomad AMR AF: 0.444

Gnomad ASJ AF: 0.390

Gnomad EAS AF: 0.0604

Gnomad SAS AF: 0.373

Gnomad FIN AF: 0.433

Gnomad MID AF: 0.399

Gnomad NFE AF: 0.463

Gnomad OTH AF: 0.384

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

GnomAD4 genome AF: 0.387 AC: 58800 AN: 152108 Hom.: 12192 Cov.: 32 AF XY: 0.387 AC XY: 28762 AN XY: 74358

African (AFR) AF: 0.271 AC: 11235 AN: 41502

American (AMR) AF: 0.443 AC: 6771 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.390 AC: 1352 AN: 3470

East Asian (EAS) AF: 0.0605 AC: 313 AN: 5174

South Asian (SAS) AF: 0.374 AC: 1804 AN: 4824

European-Finnish (FIN) AF: 0.433 AC: 4574 AN: 10568

Middle Eastern (MID) AF: 0.405 AC: 119 AN: 294

European-Non Finnish (NFE) AF: 0.463 AC: 31481 AN: 67976

Other (OTH) AF: 0.383 AC: 810 AN: 2114

Alfa AF: 0.432 Hom.: 63594

Bravo AF: 0.380

Asia WGS AF: 0.223 AC: 776 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	1.4
DANN	Benign	0.61
PhyloP100		0.026

Splicing

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

Other links and lift over

dbSNP: rs1869151; hg19: chr3-132614374;