rs17572757

Variant names:

• chr5-175632710-T-C
• rs17572757

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 0.058 in 152,236 control chromosomes in the GnomAD database, including 270 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 0.058 (270 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.56
• Publications: 3 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.0701 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: 0.0580 AC: 8829 AN: 152118 Hom.: 273 Cov.: 32

Gnomad AFR AF: 0.0725

Gnomad AMI AF: 0.105

Gnomad AMR AF: 0.0377

Gnomad ASJ AF: 0.0179

Gnomad EAS AF: 0.00423

Gnomad SAS AF: 0.0263

Gnomad FIN AF: 0.0780

Gnomad MID AF: 0.0538

Gnomad NFE AF: 0.0588

Gnomad OTH AF: 0.0469

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

GnomAD4 genome AF: 0.0580 AC: 8829 AN: 152236 Hom.: 270 Cov.: 32 AF XY: 0.0582 AC XY: 4333 AN XY: 74442

African (AFR) AF: 0.0722 AC: 3000 AN: 41534

American (AMR) AF: 0.0377 AC: 576 AN: 15298

Ashkenazi Jewish (ASJ) AF: 0.0179 AC: 62 AN: 3468

East Asian (EAS) AF: 0.00424 AC: 22 AN: 5186

South Asian (SAS) AF: 0.0266 AC: 128 AN: 4820

European-Finnish (FIN) AF: 0.0780 AC: 827 AN: 10608

Middle Eastern (MID) AF: 0.0544 AC: 16 AN: 294

European-Non Finnish (NFE) AF: 0.0588 AC: 4000 AN: 68004

Other (OTH) AF: 0.0483 AC: 102 AN: 2112

Alfa AF: 0.0568 Hom.: 482

Bravo AF: 0.0549

Asia WGS AF: 0.0380 AC: 133 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	0.014
DANN	Benign	0.23
PhyloP100		-1.6

Splicing

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

Other links and lift over

dbSNP: rs17572757; hg19: chr5-175059713;