rs4794008

Variant names:

• chr17-48971599-C-T
• rs4794008

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 7 publications found

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

 

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

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

African (AFR) AF: 0.155 AC: 6415 AN: 41470

American (AMR) AF: 0.373 AC: 5694 AN: 15260

Ashkenazi Jewish (ASJ) AF: 0.365 AC: 1265 AN: 3468

East Asian (EAS) AF: 0.225 AC: 1157 AN: 5144

South Asian (SAS) AF: 0.224 AC: 1078 AN: 4812

European-Finnish (FIN) AF: 0.235 AC: 2483 AN: 10558

Middle Eastern (MID) AF: 0.323 AC: 95 AN: 294

European-Non Finnish (NFE) AF: 0.293 AC: 19940 AN: 67956

Other (OTH) AF: 0.271 AC: 570 AN: 2104

Alfa AF: 0.285 Hom.: 11307

Bravo AF: 0.264

Asia WGS AF: 0.240 AC: 835 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.74
CADD	Benign	8.5
DANN	Benign	0.76
PhyloP100		-0.42

Splicing

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

Other links and lift over

dbSNP: rs4794008; hg19: chr17-47048961;