rs6502618

Positions:

• chr17-17843427-A-G

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 0.539 in 152,146 control chromosomes in the GnomAD database, including 23,278 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 0.54 (23278 hom., cov: 34)
  • Exomes 𝑓: 0.70 (2 hom.)
  • Failed GnomAD Quality Control
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.18

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.626 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: 0.539 AC: 81988 AN: 152026 Hom.: 23263 Cov.: 34

Gnomad AFR AF: 0.500

Gnomad AMI AF: 0.546

Gnomad AMR AF: 0.464

Gnomad ASJ AF: 0.552

Gnomad EAS AF: 0.0652

Gnomad SAS AF: 0.272

Gnomad FIN AF: 0.562

Gnomad MID AF: 0.576

Gnomad NFE AF: 0.631

Gnomad OTH AF: 0.536

GnomAD4 exome Data not reliable, filtered out with message: AS_VQSR AF: 0.700 AC: 7 AN: 10 Hom.: 2 AF XY: 0.667 AC XY: 4 AN XY: 6

Gnomad4 FIN exome AF: 0.750

Gnomad4 NFE exome AF: 0.667

GnomAD4 genome AF: 0.539 AC: 82052 AN: 152146 Hom.: 23278 Cov.: 34 AF XY: 0.527 AC XY: 39176 AN XY: 74362

Gnomad4 AFR AF: 0.500

Gnomad4 AMR AF: 0.464

Gnomad4 ASJ AF: 0.552

Gnomad4 EAS AF: 0.0652

Gnomad4 SAS AF: 0.273

Gnomad4 FIN AF: 0.562

Gnomad4 NFE AF: 0.631

Gnomad4 OTH AF: 0.536

Alfa AF: 0.574 Hom.: 3163

Bravo AF: 0.531

Asia WGS AF: 0.247 AC: 864 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	0.082
DANN	Benign	0.58

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6502618; hg19: chr17-17746741;