rs17015014

Variant names:

• chr4-141807619-G-C
• rs17015014

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 0.162 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

ACMG classification

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt

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

Gnomad4 AFR AF: 0.0900

Gnomad4 AMR AF: 0.353

Gnomad4 ASJ AF: 0.110

Gnomad4 EAS AF: 0.499

Gnomad4 SAS AF: 0.192

Gnomad4 FIN AF: 0.125

Gnomad4 NFE AF: 0.145

Gnomad4 OTH AF: 0.151

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 v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs17015014; hg19: chr4-142728772;