4-28888356-C-A

Variant names:

• chr4-28888356-C-A
• rs13128291

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 0.517 in 151,960 control chromosomes in the GnomAD database, including 21,873 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 0.52 (21873 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0200
• Publications: 0 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.01).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.816 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.517 AC: 78554 AN: 151842 Hom.: 21851 Cov.: 32

Gnomad AFR AF: 0.311

Gnomad AMI AF: 0.521

Gnomad AMR AF: 0.621

Gnomad ASJ AF: 0.632

Gnomad EAS AF: 0.837

Gnomad SAS AF: 0.586

Gnomad FIN AF: 0.599

Gnomad MID AF: 0.614

Gnomad NFE AF: 0.570

Gnomad OTH AF: 0.548

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

GnomAD4 genome AF: 0.517 AC: 78626 AN: 151960 Hom.: 21873 Cov.: 32 AF XY: 0.525 AC XY: 38946 AN XY: 74248

African (AFR) AF: 0.312 AC: 12917 AN: 41428

American (AMR) AF: 0.621 AC: 9481 AN: 15266

Ashkenazi Jewish (ASJ) AF: 0.632 AC: 2194 AN: 3470

East Asian (EAS) AF: 0.837 AC: 4323 AN: 5164

South Asian (SAS) AF: 0.587 AC: 2830 AN: 4822

European-Finnish (FIN) AF: 0.599 AC: 6314 AN: 10534

Middle Eastern (MID) AF: 0.616 AC: 181 AN: 294

European-Non Finnish (NFE) AF: 0.570 AC: 38744 AN: 67956

Other (OTH) AF: 0.552 AC: 1167 AN: 2114

Alfa AF: 0.551 Hom.: 18829

Bravo AF: 0.512

Asia WGS AF: 0.711 AC: 2473 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.41
DANN	Benign	0.54
PhyloP100		0.020

Splicing

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

Other links and lift over

dbSNP: rs13128291; hg19: chr4-28889978;