4-28659234-T-C

Variant names:

• chr4-28659234-T-C
• rs9996729
• ENST00000730159.1:n.145+19707A>G

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000730159.1(ENSG00000286141):​n.145+19707A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.798 in 152,184 control chromosomes in the GnomAD database, including 48,587 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 0.80 (48587 hom., cov: 34)
• Consequence: ENSG00000286141 ENST00000730159.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.328
• Publications: 2 publications found

Genes affected

ENSG00000286141 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.922 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000730159.1. You can select a different transcript below to see updated ACMG assignments.

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
	ENSG00000286141	ENST00000730159.1		n.145+19707A>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.798 AC: 121294 AN: 152066 Hom.: 48551 Cov.: 34

Gnomad AFR AF: 0.733

Gnomad AMI AF: 0.864

Gnomad AMR AF: 0.811

Gnomad ASJ AF: 0.863

Gnomad EAS AF: 0.944

Gnomad SAS AF: 0.911

Gnomad FIN AF: 0.813

Gnomad MID AF: 0.876

Gnomad NFE AF: 0.808

Gnomad OTH AF: 0.803

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

GnomAD4 genome AF: 0.798 AC: 121386 AN: 152184 Hom.: 48587 Cov.: 34 AF XY: 0.800 AC XY: 59534 AN XY: 74396

African (AFR) AF: 0.733 AC: 30431 AN: 41508

American (AMR) AF: 0.812 AC: 12412 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.863 AC: 2996 AN: 3470

East Asian (EAS) AF: 0.944 AC: 4892 AN: 5182

South Asian (SAS) AF: 0.911 AC: 4401 AN: 4830

European-Finnish (FIN) AF: 0.813 AC: 8614 AN: 10600

Middle Eastern (MID) AF: 0.877 AC: 256 AN: 292

European-Non Finnish (NFE) AF: 0.807 AC: 54896 AN: 67984

Other (OTH) AF: 0.804 AC: 1700 AN: 2114

Alfa AF: 0.807 Hom.: 62466

Bravo AF: 0.793

Asia WGS AF: 0.913 AC: 3168 AN: 3472

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	6.4
DANN	Benign	0.49
PhyloP100		0.33

Splicing

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

Other links and lift over

dbSNP: rs9996729; hg19: chr4-28660856;