rs17015014

Variant names:

• chr4-141807619-G-C
• rs17015014

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 0.162 in 152,120 control chromosomes in the GnomAD database, including 2,903 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 0.16 (2903 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.05
• Publications: 8 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.483 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: 0.162 AC: 24635 AN: 152002 Hom.: 2892 Cov.: 32

Gnomad AFR AF: 0.0902

Gnomad AMI AF: 0.105

Gnomad AMR AF: 0.352

Gnomad ASJ AF: 0.110

Gnomad EAS AF: 0.499

Gnomad SAS AF: 0.193

Gnomad FIN AF: 0.125

Gnomad MID AF: 0.123

Gnomad NFE AF: 0.145

Gnomad OTH AF: 0.149

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

GnomAD4 genome AF: 0.162 AC: 24659 AN: 152120 Hom.: 2903 Cov.: 32 AF XY: 0.167 AC XY: 12411 AN XY: 74368

African (AFR) AF: 0.0900 AC: 3736 AN: 41512

American (AMR) AF: 0.353 AC: 5389 AN: 15260

Ashkenazi Jewish (ASJ) AF: 0.110 AC: 383 AN: 3468

East Asian (EAS) AF: 0.499 AC: 2573 AN: 5160

South Asian (SAS) AF: 0.192 AC: 928 AN: 4826

European-Finnish (FIN) AF: 0.125 AC: 1327 AN: 10590

Middle Eastern (MID) AF: 0.133 AC: 39 AN: 294

European-Non Finnish (NFE) AF: 0.145 AC: 9868 AN: 67984

Other (OTH) AF: 0.151 AC: 320 AN: 2116

Alfa AF: 0.156 Hom.: 293

Bravo AF: 0.182

Asia WGS AF: 0.312 AC: 1084 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.21
DANN	Benign	0.43
PhyloP100		-1.0

Splicing

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

Other links and lift over

dbSNP: rs17015014; hg19: chr4-142728772;