5-170739590-A-T

Variant names:

• chr5-170739590-A-T
• rs17673653

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 0.166 in 152,118 control chromosomes in the GnomAD database, including 3,930 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 0.17 (3930 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.368
• Publications: 4 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.791 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Frequencies

GnomAD3 genomes AF: 0.166 AC: 25278 AN: 152000 Hom.: 3925 Cov.: 32

Gnomad AFR AF: 0.0479

Gnomad AMI AF: 0.137

Gnomad AMR AF: 0.320

Gnomad ASJ AF: 0.100

Gnomad EAS AF: 0.811

Gnomad SAS AF: 0.359

Gnomad FIN AF: 0.158

Gnomad MID AF: 0.155

Gnomad NFE AF: 0.147

Gnomad OTH AF: 0.155

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

GnomAD4 genome AF: 0.166 AC: 25292 AN: 152118 Hom.: 3930 Cov.: 32 AF XY: 0.177 AC XY: 13191 AN XY: 74358

African (AFR) AF: 0.0478 AC: 1986 AN: 41530

American (AMR) AF: 0.321 AC: 4903 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.100 AC: 347 AN: 3468

East Asian (EAS) AF: 0.811 AC: 4173 AN: 5144

South Asian (SAS) AF: 0.359 AC: 1724 AN: 4806

European-Finnish (FIN) AF: 0.158 AC: 1668 AN: 10590

Middle Eastern (MID) AF: 0.153 AC: 45 AN: 294

European-Non Finnish (NFE) AF: 0.147 AC: 9989 AN: 67966

Other (OTH) AF: 0.157 AC: 332 AN: 2116

Alfa AF: 0.0774 Hom.: 106

Bravo AF: 0.175

Asia WGS AF: 0.519 AC: 1802 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.97
DANN	Benign	0.56
PhyloP100		-0.37

Splicing

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

Other links and lift over

dbSNP: rs17673653; hg19: chr5-170166594;