rs17525374

Variant names:

• chr4-167897559-G-A
• rs17525374

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 0.147 in 150,924 control chromosomes in the GnomAD database, including 1,922 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 0.15 (1922 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.54
• Publications: 4 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.193 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: 0.147 AC: 22190 AN: 150820 Hom.: 1922 Cov.: 32

Gnomad AFR AF: 0.0829

Gnomad AMI AF: 0.253

Gnomad AMR AF: 0.123

Gnomad ASJ AF: 0.188

Gnomad EAS AF: 0.0484

Gnomad SAS AF: 0.0753

Gnomad FIN AF: 0.172

Gnomad MID AF: 0.198

Gnomad NFE AF: 0.196

Gnomad OTH AF: 0.172

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

GnomAD4 genome AF: 0.147 AC: 22189 AN: 150924 Hom.: 1922 Cov.: 32 AF XY: 0.144 AC XY: 10601 AN XY: 73622

African (AFR) AF: 0.0827 AC: 3396 AN: 41088

American (AMR) AF: 0.123 AC: 1863 AN: 15158

Ashkenazi Jewish (ASJ) AF: 0.188 AC: 650 AN: 3462

East Asian (EAS) AF: 0.0487 AC: 250 AN: 5134

South Asian (SAS) AF: 0.0762 AC: 365 AN: 4790

European-Finnish (FIN) AF: 0.172 AC: 1765 AN: 10264

Middle Eastern (MID) AF: 0.194 AC: 55 AN: 284

European-Non Finnish (NFE) AF: 0.196 AC: 13260 AN: 67748

Other (OTH) AF: 0.170 AC: 355 AN: 2088

Alfa AF: 0.180 Hom.: 9544

Bravo AF: 0.143

Asia WGS AF: 0.0570 AC: 201 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	0.18
DANN	Benign	0.65
PhyloP100		-1.5

Splicing

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

Other links and lift over

dbSNP: rs17525374; hg19: chr4-168818710;