rs4315391

Variant names:

• chr17-17426414-G-A
• rs4315391

Your query was ambiguous. Multiple possible variants found:

• chr17-17426414-G-A
• chr17-17426414-G-C

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 0.425 in 152,126 control chromosomes in the GnomAD database, including 17,602 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 0.42 (17602 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.50
• Publications: 4 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.78).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.775 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: 0.424 AC: 64527 AN: 152008 Hom.: 17558 Cov.: 33

Gnomad AFR AF: 0.782

Gnomad AMI AF: 0.304

Gnomad AMR AF: 0.277

Gnomad ASJ AF: 0.201

Gnomad EAS AF: 0.167

Gnomad SAS AF: 0.347

Gnomad FIN AF: 0.270

Gnomad MID AF: 0.396

Gnomad NFE AF: 0.304

Gnomad OTH AF: 0.377

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

GnomAD4 genome AF: 0.425 AC: 64625 AN: 152126 Hom.: 17602 Cov.: 33 AF XY: 0.416 AC XY: 30946 AN XY: 74370

African (AFR) AF: 0.782 AC: 32460 AN: 41510

American (AMR) AF: 0.276 AC: 4224 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.201 AC: 698 AN: 3468

East Asian (EAS) AF: 0.167 AC: 863 AN: 5182

South Asian (SAS) AF: 0.347 AC: 1674 AN: 4822

European-Finnish (FIN) AF: 0.270 AC: 2859 AN: 10572

Middle Eastern (MID) AF: 0.398 AC: 117 AN: 294

European-Non Finnish (NFE) AF: 0.304 AC: 20652 AN: 67974

Other (OTH) AF: 0.380 AC: 802 AN: 2112

Alfa AF: 0.332 Hom.: 15788

Bravo AF: 0.440

Asia WGS AF: 0.326 AC: 1134 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.78
CADD	Benign	0.34
DANN	Benign	0.64
PhyloP100		-1.5

Splicing

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

Other links and lift over

dbSNP: rs4315391; hg19: chr17-17329728;