rs4794008

Variant names:

• chr17-48971599-C-T
• rs4794008

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 0.256 in 151,976 control chromosomes in the GnomAD database, including 5,534 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 0.26 (5534 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.425

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.74).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.365 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: 0.256 AC: 38905 AN: 151858 Hom.: 5530 Cov.: 31

Gnomad AFR AF: 0.154

Gnomad AMI AF: 0.263

Gnomad AMR AF: 0.373

Gnomad ASJ AF: 0.365

Gnomad EAS AF: 0.225

Gnomad SAS AF: 0.222

Gnomad FIN AF: 0.235

Gnomad MID AF: 0.326

Gnomad NFE AF: 0.293

Gnomad OTH AF: 0.273

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

GnomAD4 genome AF: 0.256 AC: 38936 AN: 151976 Hom.: 5534 Cov.: 31 AF XY: 0.256 AC XY: 19013 AN XY: 74280

Gnomad4 AFR AF: 0.155

Gnomad4 AMR AF: 0.373

Gnomad4 ASJ AF: 0.365

Gnomad4 EAS AF: 0.225

Gnomad4 SAS AF: 0.224

Gnomad4 FIN AF: 0.235

Gnomad4 NFE AF: 0.293

Gnomad4 OTH AF: 0.271

Alfa AF: 0.290 Hom.: 7393

Bravo AF: 0.264

Asia WGS AF: 0.240 AC: 835 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.74
CADD	Benign	8.5
DANN	Benign	0.76

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4794008; hg19: chr17-47048961;