5-28755886-T-C

Variant names:

• chr5-28755886-T-C
• rs967079
• ENST00000653909.1:n.322-45912A>G

Variant summary

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

The ENST00000653909.1(ENSG00000250453):​n.322-45912A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.568 in 151,826 control chromosomes in the GnomAD database, including 24,943 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 0.57 (24943 hom., cov: 32)
• Consequence: ENSG00000250453 ENST00000653909.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.125
• Publications: 4 publications found

Genes affected

ENSG00000250453 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.83).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.726 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000653909.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000250453	ENST00000653909.1		n.322-45912A>G		intron	N/A
	ENSG00000250453	ENST00000660682.1		n.337-45912A>G		intron	N/A
	ENSG00000250453	ENST00000849332.1		n.341-45912A>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.568 AC: 86194 AN: 151706 Hom.: 24945 Cov.: 32

Gnomad AFR AF: 0.458

Gnomad AMI AF: 0.576

Gnomad AMR AF: 0.623

Gnomad ASJ AF: 0.667

Gnomad EAS AF: 0.746

Gnomad SAS AF: 0.617

Gnomad FIN AF: 0.608

Gnomad MID AF: 0.703

Gnomad NFE AF: 0.593

Gnomad OTH AF: 0.589

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

GnomAD4 genome AF: 0.568 AC: 86234 AN: 151826 Hom.: 24943 Cov.: 32 AF XY: 0.574 AC XY: 42558 AN XY: 74158

African (AFR) AF: 0.458 AC: 18975 AN: 41400

American (AMR) AF: 0.624 AC: 9477 AN: 15186

Ashkenazi Jewish (ASJ) AF: 0.667 AC: 2316 AN: 3470

East Asian (EAS) AF: 0.746 AC: 3841 AN: 5148

South Asian (SAS) AF: 0.616 AC: 2960 AN: 4806

European-Finnish (FIN) AF: 0.608 AC: 6423 AN: 10556

Middle Eastern (MID) AF: 0.694 AC: 204 AN: 294

European-Non Finnish (NFE) AF: 0.593 AC: 40276 AN: 67938

Other (OTH) AF: 0.585 AC: 1237 AN: 2116

Alfa AF: 0.576 Hom.: 8681

Bravo AF: 0.568

Asia WGS AF: 0.624 AC: 2171 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	3.3
DANN	Benign	0.51
PhyloP100		0.13

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs967079;

hg19: chr5-28755993;