3-187921587-A-C

Variant names:

• chr3-187921587-A-C
• rs763342

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 151,916 control chromosomes in the GnomAD database, including 8,690 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 (8690 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0780
• Publications: 13 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.77).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.501 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

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

Ensembl Transcripts

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

Frequencies

GnomAD3 genomes AF: 0.333 AC: 50592 AN: 151798 Hom.: 8690 Cov.: 32

Gnomad AFR AF: 0.302

Gnomad AMI AF: 0.400

Gnomad AMR AF: 0.324

Gnomad ASJ AF: 0.418

Gnomad EAS AF: 0.518

Gnomad SAS AF: 0.273

Gnomad FIN AF: 0.369

Gnomad MID AF: 0.411

Gnomad NFE AF: 0.333

Gnomad OTH AF: 0.345

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

GnomAD4 genome AF: 0.333 AC: 50608 AN: 151916 Hom.: 8690 Cov.: 32 AF XY: 0.335 AC XY: 24902 AN XY: 74248

African (AFR) AF: 0.302 AC: 12488 AN: 41404

American (AMR) AF: 0.324 AC: 4952 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.418 AC: 1451 AN: 3470

East Asian (EAS) AF: 0.518 AC: 2670 AN: 5156

South Asian (SAS) AF: 0.273 AC: 1316 AN: 4816

European-Finnish (FIN) AF: 0.369 AC: 3891 AN: 10544

Middle Eastern (MID) AF: 0.418 AC: 123 AN: 294

European-Non Finnish (NFE) AF: 0.333 AC: 22633 AN: 67940

Other (OTH) AF: 0.341 AC: 719 AN: 2106

Alfa AF: 0.331 Hom.: 37223

Bravo AF: 0.332

Asia WGS AF: 0.346 AC: 1205 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.77
CADD	Benign	5.3
DANN	Benign	0.59
PhyloP100		0.078

Splicing

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

Other links and lift over

dbSNP: rs763342; hg19: chr3-187639375;