rs4793513

Variant names:

• chr17-70922156-G-A
• rs4793513

Your query was ambiguous. Multiple possible variants found:

• chr17-70922156-G-A
• chr17-70922156-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 0.191 in 152,060 control chromosomes in the GnomAD database, including 2,941 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 0.19 (2941 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.644
• Publications: 4 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.236 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Frequencies

GnomAD3 genomes AF: 0.191 AC: 28949 AN: 151942 Hom.: 2940 Cov.: 32

Gnomad AFR AF: 0.240

Gnomad AMI AF: 0.174

Gnomad AMR AF: 0.232

Gnomad ASJ AF: 0.185

Gnomad EAS AF: 0.117

Gnomad SAS AF: 0.134

Gnomad FIN AF: 0.156

Gnomad MID AF: 0.228

Gnomad NFE AF: 0.167

Gnomad OTH AF: 0.184

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

GnomAD4 genome AF: 0.191 AC: 28981 AN: 152060 Hom.: 2941 Cov.: 32 AF XY: 0.190 AC XY: 14133 AN XY: 74340

African (AFR) AF: 0.240 AC: 9952 AN: 41450

American (AMR) AF: 0.232 AC: 3541 AN: 15264

Ashkenazi Jewish (ASJ) AF: 0.185 AC: 640 AN: 3468

East Asian (EAS) AF: 0.117 AC: 605 AN: 5172

South Asian (SAS) AF: 0.135 AC: 650 AN: 4826

European-Finnish (FIN) AF: 0.156 AC: 1644 AN: 10570

Middle Eastern (MID) AF: 0.211 AC: 62 AN: 294

European-Non Finnish (NFE) AF: 0.167 AC: 11341 AN: 67994

Other (OTH) AF: 0.183 AC: 387 AN: 2110

Alfa AF: 0.155 Hom.: 1032

Bravo AF: 0.201

Asia WGS AF: 0.144 AC: 501 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.15
DANN	Benign	0.44
PhyloP100		-0.64

Splicing

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

Other links and lift over

dbSNP: rs4793513; hg19: chr17-68918297;