rs2325717

Variant names:

• chr17-47790438-T-C
• rs2325717

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 0.0738 in 152,324 control chromosomes in the GnomAD database, including 535 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 (535 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.934

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.68).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.202 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: 0.0739 AC: 11250 AN: 152206 Hom.: 533 Cov.: 32

Gnomad AFR AF: 0.0285

Gnomad AMI AF: 0.0482

Gnomad AMR AF: 0.103

Gnomad ASJ AF: 0.0858

Gnomad EAS AF: 0.0580

Gnomad SAS AF: 0.213

Gnomad FIN AF: 0.0729

Gnomad MID AF: 0.0443

Gnomad NFE AF: 0.0866

Gnomad OTH AF: 0.0718

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

GnomAD4 genome AF: 0.0738 AC: 11244 AN: 152324 Hom.: 535 Cov.: 32 AF XY: 0.0768 AC XY: 5720 AN XY: 74476

Gnomad4 AFR AF: 0.0284

Gnomad4 AMR AF: 0.102

Gnomad4 ASJ AF: 0.0858

Gnomad4 EAS AF: 0.0580

Gnomad4 SAS AF: 0.212

Gnomad4 FIN AF: 0.0729

Gnomad4 NFE AF: 0.0866

Gnomad4 OTH AF: 0.0715

Alfa AF: 0.0790 Hom.: 98

Bravo AF: 0.0709

Asia WGS AF: 0.143 AC: 500 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.68
CADD	Benign	8.7
DANN	Benign	0.91

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2325717; hg19: chr17-45867804;