chr3-49352817-A-G

Variant names:

• chr3-49352817-A-G
• rs17650792

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 0.428 in 151,910 control chromosomes in the GnomAD database, including 15,329 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 0.43 (15329 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0860
• Publications: 29 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.908 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: 0.428 AC: 64922 AN: 151792 Hom.: 15314 Cov.: 31

Gnomad AFR AF: 0.311

Gnomad AMI AF: 0.533

Gnomad AMR AF: 0.574

Gnomad ASJ AF: 0.344

Gnomad EAS AF: 0.930

Gnomad SAS AF: 0.679

Gnomad FIN AF: 0.346

Gnomad MID AF: 0.383

Gnomad NFE AF: 0.425

Gnomad OTH AF: 0.426

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

GnomAD4 genome AF: 0.428 AC: 64963 AN: 151910 Hom.: 15329 Cov.: 31 AF XY: 0.433 AC XY: 32174 AN XY: 74244

African (AFR) AF: 0.311 AC: 12873 AN: 41410

American (AMR) AF: 0.575 AC: 8773 AN: 15256

Ashkenazi Jewish (ASJ) AF: 0.344 AC: 1194 AN: 3468

East Asian (EAS) AF: 0.930 AC: 4804 AN: 5166

South Asian (SAS) AF: 0.678 AC: 3264 AN: 4812

European-Finnish (FIN) AF: 0.346 AC: 3652 AN: 10544

Middle Eastern (MID) AF: 0.378 AC: 111 AN: 294

European-Non Finnish (NFE) AF: 0.425 AC: 28898 AN: 67944

Other (OTH) AF: 0.432 AC: 909 AN: 2106

Alfa AF: 0.432 Hom.: 18306

Bravo AF: 0.441

Asia WGS AF: 0.770 AC: 2671 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	5.3
DANN	Benign	0.76
PhyloP100		-0.086

Splicing

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

Other links and lift over

dbSNP: rs17650792; hg19: chr3-49390250;