rs17746001

Variant names:

• chr4-179734472-C-T
• rs17746001

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 0.0547 in 152,204 control chromosomes in the GnomAD database, including 358 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 0.055 (358 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0910

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.151 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: 0.0546 AC: 8311 AN: 152086 Hom.: 356 Cov.: 32

Gnomad AFR AF: 0.0228

Gnomad AMI AF: 0.0439

Gnomad AMR AF: 0.157

Gnomad ASJ AF: 0.0881

Gnomad EAS AF: 0.0523

Gnomad SAS AF: 0.0939

Gnomad FIN AF: 0.0346

Gnomad MID AF: 0.133

Gnomad NFE AF: 0.0491

Gnomad OTH AF: 0.0746

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

GnomAD4 genome AF: 0.0547 AC: 8321 AN: 152204 Hom.: 358 Cov.: 32 AF XY: 0.0579 AC XY: 4308 AN XY: 74408

Gnomad4 AFR AF: 0.0227

Gnomad4 AMR AF: 0.156

Gnomad4 ASJ AF: 0.0881

Gnomad4 EAS AF: 0.0523

Gnomad4 SAS AF: 0.0941

Gnomad4 FIN AF: 0.0346

Gnomad4 NFE AF: 0.0491

Gnomad4 OTH AF: 0.0795

Alfa AF: 0.0550 Hom.: 324

Bravo AF: 0.0610

Asia WGS AF: 0.0820 AC: 286 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	1.7
DANN	Benign	0.37

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs17746001; hg19: chr4-180655625;