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. Variant got -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

ACMG classification

Verdict is Benign. Variant got -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.

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: 0.119 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

Gnomad4 AFR AF: 0.0337

Gnomad4 AMR AF: 0.200

Gnomad4 ASJ AF: 0.143

Gnomad4 EAS AF: 0.0560

Gnomad4 SAS AF: 0.156

Gnomad4 FIN AF: 0.198

Gnomad4 NFE AF: 0.141

Gnomad4 OTH AF: 0.140

Alfa AF: 0.125 Hom.: 777

Bravo AF: 0.118

Asia WGS AF: 0.0940 AC: 328 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs17363613; hg19: chr2-5733431;