rs17363613

Variant names:

• chr2-5593299-C-A
• rs17363613

Your query was ambiguous. Multiple possible variants found:

• chr2-5593299-C-A
• chr2-5593299-C-T

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 0.119 in 152,112 control chromosomes in the GnomAD database, including 1,355 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 0.12 (1355 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.70
• Publications: 0 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.82).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.194 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: 0.119 AC: 18114 AN: 151994 Hom.: 1349 Cov.: 32

Gnomad AFR AF: 0.0338

Gnomad AMI AF: 0.180

Gnomad AMR AF: 0.199

Gnomad ASJ AF: 0.143

Gnomad EAS AF: 0.0562

Gnomad SAS AF: 0.154

Gnomad FIN AF: 0.198

Gnomad MID AF: 0.144

Gnomad NFE AF: 0.140

Gnomad OTH AF: 0.142

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

GnomAD4 genome AF: 0.119 AC: 18125 AN: 152112 Hom.: 1355 Cov.: 32 AF XY: 0.123 AC XY: 9108 AN XY: 74346

African (AFR) AF: 0.0337 AC: 1400 AN: 41530

American (AMR) AF: 0.200 AC: 3051 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.143 AC: 497 AN: 3470

East Asian (EAS) AF: 0.0560 AC: 290 AN: 5180

South Asian (SAS) AF: 0.156 AC: 751 AN: 4820

European-Finnish (FIN) AF: 0.198 AC: 2083 AN: 10532

Middle Eastern (MID) AF: 0.141 AC: 41 AN: 290

European-Non Finnish (NFE) AF: 0.141 AC: 9554 AN: 67998

Other (OTH) AF: 0.140 AC: 295 AN: 2108

Alfa AF: 0.128 Hom.: 1166

Bravo AF: 0.118

Asia WGS AF: 0.0940 AC: 328 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	0.12
DANN	Benign	0.51
PhyloP100		-1.7

Splicing

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

Other links and lift over

dbSNP: rs17363613; hg19: chr2-5733431;