rs17746001

Variant names:

• chr4-179734472-C-T
• rs17746001

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 0.0547 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
• Publications: 5 publications found

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

 

RefSeq Transcripts

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

Ensembl Transcripts

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

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

African (AFR) AF: 0.0227 AC: 944 AN: 41546

American (AMR) AF: 0.156 AC: 2390 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.0881 AC: 306 AN: 3472

East Asian (EAS) AF: 0.0523 AC: 270 AN: 5166

South Asian (SAS) AF: 0.0941 AC: 453 AN: 4812

European-Finnish (FIN) AF: 0.0346 AC: 367 AN: 10608

Middle Eastern (MID) AF: 0.143 AC: 42 AN: 294

European-Non Finnish (NFE) AF: 0.0491 AC: 3341 AN: 67998

Other (OTH) AF: 0.0795 AC: 168 AN: 2112

Alfa AF: 0.0546 Hom.: 637

Bravo AF: 0.0610

Asia WGS AF: 0.0820 AC: 286 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	1.7
DANN	Benign	0.37
PhyloP100		0.091

Splicing

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

Other links and lift over

dbSNP: rs17746001; hg19: chr4-180655625;