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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC107986409	XR_001742621.1	n.183-5714T>C		intron_variant	Intron 2 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000250453	ENST00000653909.1	n.322-45912A>G		intron_variant	Intron 1 of 4
ENSG00000250453	ENST00000660682.1	n.337-45912A>G		intron_variant	Intron 1 of 4
ENSG00000250453	ENST00000849332.1	n.341-45912A>G		intron_variant	Intron 1 of 4

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 v4.3

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

Other links and lift over

dbSNP: rs967079; hg19: chr5-28755993;