rs17746001

Positions:

• chr4-179734472-C-T

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: intergenic_region
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0910

Genes affected

(HGNC:):

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/exons	MANE	Protein	UniProt
		n.179734472C>T		intergenic_region

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	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;