rs779503

Variant names:

• chr3-191701204-A-G
• rs779503

Your query was ambiguous. Multiple possible variants found:

• chr3-191701204-A-G
• chr3-191701204-A-T

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 0.304 in 151,976 control chromosomes in the GnomAD database, including 7,335 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 0.30 (7335 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.436

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.02).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.397 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: 0.304 AC: 46159 AN: 151858 Hom.: 7326 Cov.: 31

Gnomad AFR AF: 0.205

Gnomad AMI AF: 0.435

Gnomad AMR AF: 0.277

Gnomad ASJ AF: 0.361

Gnomad EAS AF: 0.411

Gnomad SAS AF: 0.393

Gnomad FIN AF: 0.415

Gnomad MID AF: 0.222

Gnomad NFE AF: 0.335

Gnomad OTH AF: 0.283

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

GnomAD4 genome AF: 0.304 AC: 46187 AN: 151976 Hom.: 7335 Cov.: 31 AF XY: 0.310 AC XY: 23065 AN XY: 74284

Gnomad4 AFR AF: 0.204

Gnomad4 AMR AF: 0.277

Gnomad4 ASJ AF: 0.361

Gnomad4 EAS AF: 0.412

Gnomad4 SAS AF: 0.393

Gnomad4 FIN AF: 0.415

Gnomad4 NFE AF: 0.335

Gnomad4 OTH AF: 0.286

Alfa AF: 0.306 Hom.: 3807

Bravo AF: 0.289

Asia WGS AF: 0.411 AC: 1425 AN: 3472

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.66
DANN	Benign	0.32

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs779503; hg19: chr3-191418993; COSMIC: COSV67202675;