rs17658562

chr6-18957598-C-T

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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	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;