rs17008504

chr4-124718662-T-A

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 0.0455 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

ACMG classification

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt

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

Gnomad4 AFR AF: 0.0580

Gnomad4 AMR AF: 0.0547

Gnomad4 ASJ AF: 0.00691

Gnomad4 EAS AF: 0.243

Gnomad4 SAS AF: 0.0375

Gnomad4 FIN AF: 0.0757

Gnomad4 NFE AF: 0.0191

Gnomad4 OTH AF: 0.0440

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 v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
Cadd	Benign	5.6
Dann	Benign	0.40

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs17008504; hg19: chr4-125639817;