rs4793501

Positions:

• chr17-70722593-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 0.635 in 151,918 control chromosomes in the GnomAD database, including 31,522 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 0.64 (31522 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.149

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.778 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: 0.635 AC: 96404 AN: 151800 Hom.: 31484 Cov.: 31

Gnomad AFR AF: 0.785

Gnomad AMI AF: 0.411

Gnomad AMR AF: 0.624

Gnomad ASJ AF: 0.627

Gnomad EAS AF: 0.400

Gnomad SAS AF: 0.521

Gnomad FIN AF: 0.521

Gnomad MID AF: 0.778

Gnomad NFE AF: 0.592

Gnomad OTH AF: 0.657

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

GnomAD4 genome AF: 0.635 AC: 96493 AN: 151918 Hom.: 31522 Cov.: 31 AF XY: 0.630 AC XY: 46767 AN XY: 74248

Gnomad4 AFR AF: 0.785

Gnomad4 AMR AF: 0.624

Gnomad4 ASJ AF: 0.627

Gnomad4 EAS AF: 0.400

Gnomad4 SAS AF: 0.519

Gnomad4 FIN AF: 0.521

Gnomad4 NFE AF: 0.592

Gnomad4 OTH AF: 0.657

Alfa AF: 0.605 Hom.: 37521

Bravo AF: 0.647

Asia WGS AF: 0.486 AC: 1691 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	2.9
DANN	Benign	0.60

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4793501; hg19: chr17-68718734;