rs17008504

Variant names:

• chr4-124718662-T-A
• rs17008504

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 0.0455 in 152,200 control chromosomes in the GnomAD database, including 315 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 0.046 (315 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.680
• Publications: 1 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.232 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: 0.0455 AC: 6915 AN: 152080 Hom.: 313 Cov.: 32

Gnomad AFR AF: 0.0580

Gnomad AMI AF: 0.0286

Gnomad AMR AF: 0.0542

Gnomad ASJ AF: 0.00691

Gnomad EAS AF: 0.243

Gnomad SAS AF: 0.0371

Gnomad FIN AF: 0.0757

Gnomad MID AF: 0.0160

Gnomad NFE AF: 0.0191

Gnomad OTH AF: 0.0445

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

GnomAD4 genome AF: 0.0455 AC: 6927 AN: 152200 Hom.: 315 Cov.: 32 AF XY: 0.0480 AC XY: 3569 AN XY: 74388

African (AFR) AF: 0.0580 AC: 2407 AN: 41526

American (AMR) AF: 0.0547 AC: 837 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.00691 AC: 24 AN: 3472

East Asian (EAS) AF: 0.243 AC: 1254 AN: 5154

South Asian (SAS) AF: 0.0375 AC: 181 AN: 4824

European-Finnish (FIN) AF: 0.0757 AC: 802 AN: 10596

Middle Eastern (MID) AF: 0.0137 AC: 4 AN: 292

European-Non Finnish (NFE) AF: 0.0191 AC: 1299 AN: 68020

Other (OTH) AF: 0.0440 AC: 93 AN: 2112

Alfa AF: 0.0323 Hom.: 9

Bravo AF: 0.0467

Asia WGS AF: 0.143 AC: 495 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	5.6
DANN	Benign	0.40
PhyloP100		0.68

Splicing

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

Other links and lift over

dbSNP: rs17008504; hg19: chr4-125639817;