rs2325717

Variant names:

• chr17-47790438-T-C
• rs2325717

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 0.0738 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
• Publications: 1 publications found

ACMG classification

Our verdict: Benign. The variant received -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.

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: 0.0739 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

African (AFR) AF: 0.0284 AC: 1181 AN: 41584

American (AMR) AF: 0.102 AC: 1567 AN: 15298

Ashkenazi Jewish (ASJ) AF: 0.0858 AC: 298 AN: 3472

East Asian (EAS) AF: 0.0580 AC: 300 AN: 5176

South Asian (SAS) AF: 0.212 AC: 1025 AN: 4828

European-Finnish (FIN) AF: 0.0729 AC: 774 AN: 10616

Middle Eastern (MID) AF: 0.0408 AC: 12 AN: 294

European-Non Finnish (NFE) AF: 0.0866 AC: 5892 AN: 68032

Other (OTH) AF: 0.0715 AC: 151 AN: 2112

Alfa AF: 0.0779 Hom.: 99

Bravo AF: 0.0709

Asia WGS AF: 0.143 AC: 500 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.68
CADD	Benign	8.7
DANN	Benign	0.91
PhyloP100		-0.93

Splicing

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

Other links and lift over

dbSNP: rs2325717; hg19: chr17-45867804;