rs17564315

Variant names:

• chr2-19758735-G-A
• rs17564315

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 0.147 in 152,234 control chromosomes in the GnomAD database, including 1,737 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 0.15 (1737 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.43

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.8).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.165 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: 0.147 AC: 22318 AN: 152116 Hom.: 1729 Cov.: 33

Gnomad AFR AF: 0.137

Gnomad AMI AF: 0.0692

Gnomad AMR AF: 0.141

Gnomad ASJ AF: 0.0937

Gnomad EAS AF: 0.0828

Gnomad SAS AF: 0.0656

Gnomad FIN AF: 0.151

Gnomad MID AF: 0.0759

Gnomad NFE AF: 0.168

Gnomad OTH AF: 0.146

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

GnomAD4 genome AF: 0.147 AC: 22357 AN: 152234 Hom.: 1737 Cov.: 33 AF XY: 0.143 AC XY: 10620 AN XY: 74434

Gnomad4 AFR AF: 0.137

Gnomad4 AMR AF: 0.142

Gnomad4 ASJ AF: 0.0937

Gnomad4 EAS AF: 0.0836

Gnomad4 SAS AF: 0.0659

Gnomad4 FIN AF: 0.151

Gnomad4 NFE AF: 0.168

Gnomad4 OTH AF: 0.149

Alfa AF: 0.162 Hom.: 1939

Bravo AF: 0.147

Asia WGS AF: 0.109 AC: 379 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.80
CADD	Benign	11
DANN	Benign	0.75

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs17564315; hg19: chr2-19958496;