rs17015014

Positions:

• chr4-141807619-G-C

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/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	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;