rs6501658

Positions:

• chr17-73665490-T-C

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/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	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;