rs6501658

Variant names:

• chr17-73665490-T-C
• rs6501658

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_Moderate BA1

The variant allele was found at a frequency of 0.327 in 152,080 control chromosomes in the GnomAD database, including 8,740 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 0.33 (8740 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.19

ACMG classification

Verdict is Benign. Variant got -10 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.35).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.443 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: 0.327 AC: 49656 AN: 151962 Hom.: 8708 Cov.: 32

Gnomad AFR AF: 0.447

Gnomad AMI AF: 0.372

Gnomad AMR AF: 0.371

Gnomad ASJ AF: 0.346

Gnomad EAS AF: 0.170

Gnomad SAS AF: 0.285

Gnomad FIN AF: 0.190

Gnomad MID AF: 0.253

Gnomad NFE AF: 0.279

Gnomad OTH AF: 0.308

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

GnomAD4 genome AF: 0.327 AC: 49744 AN: 152080 Hom.: 8740 Cov.: 32 AF XY: 0.322 AC XY: 23929 AN XY: 74366

Gnomad4 AFR AF: 0.448

Gnomad4 AMR AF: 0.372

Gnomad4 ASJ AF: 0.346

Gnomad4 EAS AF: 0.170

Gnomad4 SAS AF: 0.284

Gnomad4 FIN AF: 0.190

Gnomad4 NFE AF: 0.279

Gnomad4 OTH AF: 0.309

Alfa AF: 0.292 Hom.: 13135

Bravo AF: 0.350

Asia WGS AF: 0.254 AC: 884 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.35
CADD	Benign	21
DANN	Benign	0.81

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6501658; hg19: chr17-71661629;