rs763342

Variant names:

• chr3-187921587-A-C
• rs763342

Your query was ambiguous. Multiple possible variants found:

• chr3-187921587-A-C
• chr3-187921587-A-G

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 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

ACMG classification

Verdict is Benign. Variant got -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.

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: 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

Gnomad4 AFR AF: 0.302

Gnomad4 AMR AF: 0.324

Gnomad4 ASJ AF: 0.418

Gnomad4 EAS AF: 0.518

Gnomad4 SAS AF: 0.273

Gnomad4 FIN AF: 0.369

Gnomad4 NFE AF: 0.333

Gnomad4 OTH AF: 0.341

Alfa AF: 0.329 Hom.: 17664

Bravo AF: 0.332

Asia WGS AF: 0.346 AC: 1205 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs763342; hg19: chr3-187639375;