rs2325717

Positions:

• chr17-47790438-T-C

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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	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;