4-17531157-G-A

Variant names:

• chr4-17531157-G-A
• rs2535228

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 0.301 in 151,998 control chromosomes in the GnomAD database, including 7,860 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 0.30 (7860 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.346
• Publications: 8 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 (AFR) allele frequency at 95% confidence interval = 0.458 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: 0.301 AC: 45760 AN: 151880 Hom.: 7853 Cov.: 32

Gnomad AFR AF: 0.463

Gnomad AMI AF: 0.188

Gnomad AMR AF: 0.214

Gnomad ASJ AF: 0.301

Gnomad EAS AF: 0.0146

Gnomad SAS AF: 0.286

Gnomad FIN AF: 0.206

Gnomad MID AF: 0.373

Gnomad NFE AF: 0.261

Gnomad OTH AF: 0.305

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

GnomAD4 genome AF: 0.301 AC: 45789 AN: 151998 Hom.: 7860 Cov.: 32 AF XY: 0.296 AC XY: 21961 AN XY: 74274

African (AFR) AF: 0.463 AC: 19178 AN: 41416

American (AMR) AF: 0.213 AC: 3251 AN: 15268

Ashkenazi Jewish (ASJ) AF: 0.301 AC: 1046 AN: 3470

East Asian (EAS) AF: 0.0147 AC: 76 AN: 5180

South Asian (SAS) AF: 0.286 AC: 1373 AN: 4806

European-Finnish (FIN) AF: 0.206 AC: 2173 AN: 10568

Middle Eastern (MID) AF: 0.374 AC: 110 AN: 294

European-Non Finnish (NFE) AF: 0.261 AC: 17770 AN: 67972

Other (OTH) AF: 0.303 AC: 641 AN: 2114

Alfa AF: 0.288 Hom.: 10763

Bravo AF: 0.305

Asia WGS AF: 0.152 AC: 529 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	3.9
DANN	Benign	0.46
PhyloP100		0.35

Splicing

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

Other links and lift over

dbSNP: rs2535228; hg19: chr4-17532780;