rs17658562

Variant names:

• chr6-18957598-C-T
• rs17658562

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 0.0816 in 152,036 control chromosomes in the GnomAD database, including 568 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 0.082 (568 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.874

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.096 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: 0.0815 AC: 12377 AN: 151922 Hom.: 563 Cov.: 32

Gnomad AFR AF: 0.0535

Gnomad AMI AF: 0.185

Gnomad AMR AF: 0.0973

Gnomad ASJ AF: 0.125

Gnomad EAS AF: 0.0332

Gnomad SAS AF: 0.0922

Gnomad FIN AF: 0.0538

Gnomad MID AF: 0.117

Gnomad NFE AF: 0.0980

Gnomad OTH AF: 0.0946

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

GnomAD4 genome AF: 0.0816 AC: 12405 AN: 152036 Hom.: 568 Cov.: 32 AF XY: 0.0795 AC XY: 5908 AN XY: 74292

Gnomad4 AFR AF: 0.0538

Gnomad4 AMR AF: 0.0978

Gnomad4 ASJ AF: 0.125

Gnomad4 EAS AF: 0.0333

Gnomad4 SAS AF: 0.0925

Gnomad4 FIN AF: 0.0538

Gnomad4 NFE AF: 0.0980

Gnomad4 OTH AF: 0.0951

Alfa AF: 0.0870 Hom.: 118

Bravo AF: 0.0854

Asia WGS AF: 0.0740 AC: 256 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	12
DANN	Benign	0.65

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs17658562; hg19: chr6-18957829;