rs17047438

Variant names:

• chr2-117811830-C-T
• rs17047438

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 0.0737 in 152,232 control chromosomes in the GnomAD database, including 527 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 0.074 (527 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.503
• Publications: 1 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.109 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: 0.0736 AC: 11190 AN: 152114 Hom.: 524 Cov.: 32

Gnomad AFR AF: 0.0831

Gnomad AMI AF: 0.141

Gnomad AMR AF: 0.113

Gnomad ASJ AF: 0.0392

Gnomad EAS AF: 0.0518

Gnomad SAS AF: 0.0561

Gnomad FIN AF: 0.142

Gnomad MID AF: 0.0316

Gnomad NFE AF: 0.0528

Gnomad OTH AF: 0.0521

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

GnomAD4 genome AF: 0.0737 AC: 11215 AN: 152232 Hom.: 527 Cov.: 32 AF XY: 0.0780 AC XY: 5807 AN XY: 74422

African (AFR) AF: 0.0831 AC: 3451 AN: 41534

American (AMR) AF: 0.114 AC: 1739 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.0392 AC: 136 AN: 3472

East Asian (EAS) AF: 0.0515 AC: 267 AN: 5186

South Asian (SAS) AF: 0.0564 AC: 272 AN: 4826

European-Finnish (FIN) AF: 0.142 AC: 1502 AN: 10594

Middle Eastern (MID) AF: 0.0340 AC: 10 AN: 294

European-Non Finnish (NFE) AF: 0.0528 AC: 3592 AN: 68016

Other (OTH) AF: 0.0553 AC: 117 AN: 2114

Alfa AF: 0.0670 Hom.: 62

Bravo AF: 0.0715

Asia WGS AF: 0.0700 AC: 243 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	3.5
DANN	Benign	0.56
PhyloP100		0.50

Splicing

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

Other links and lift over

dbSNP: rs17047438; hg19: chr2-118569406;