5-132080368-C-A

Variant names:

• chr5-132080368-C-A
• rs25887
• ENST00000517258.1:n.*235C>A

Variant summary

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

The ENST00000517258.1(ENSG00000253067):​n.*235C>A variant causes a downstream gene change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.528 in 151,970 control chromosomes in the GnomAD database, including 21,581 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 0.53 (21581 hom., cov: 32)
• Consequence: ENSG00000253067 ENST00000517258.1 downstream_gene
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.194
• Publications: 23 publications found

Genes affected

ENSG00000253067 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.81).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.596 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
ENSG00000253067	ENST00000517258.1	n.*235C>A		downstream_gene_variant		6

Frequencies

GnomAD3 genomes AF: 0.528 AC: 80135 AN: 151852 Hom.: 21572 Cov.: 32

Gnomad AFR AF: 0.463

Gnomad AMI AF: 0.754

Gnomad AMR AF: 0.500

Gnomad ASJ AF: 0.549

Gnomad EAS AF: 0.614

Gnomad SAS AF: 0.342

Gnomad FIN AF: 0.592

Gnomad MID AF: 0.361

Gnomad NFE AF: 0.566

Gnomad OTH AF: 0.547

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

GnomAD4 genome AF: 0.528 AC: 80179 AN: 151970 Hom.: 21581 Cov.: 32 AF XY: 0.522 AC XY: 38750 AN XY: 74248

African (AFR) AF: 0.462 AC: 19145 AN: 41408

American (AMR) AF: 0.499 AC: 7631 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.549 AC: 1904 AN: 3468

East Asian (EAS) AF: 0.614 AC: 3162 AN: 5150

South Asian (SAS) AF: 0.342 AC: 1648 AN: 4822

European-Finnish (FIN) AF: 0.592 AC: 6256 AN: 10564

Middle Eastern (MID) AF: 0.371 AC: 109 AN: 294

European-Non Finnish (NFE) AF: 0.566 AC: 38476 AN: 67962

Other (OTH) AF: 0.551 AC: 1162 AN: 2108

Alfa AF: 0.556 Hom.: 101813

Bravo AF: 0.526

Asia WGS AF: 0.495 AC: 1722 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
CADD	Benign	3.2
DANN	Benign	0.56
PhyloP100		0.19

Splicing

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

Other links and lift over

dbSNP: rs25887; hg19: chr5-131416061; COSMIC: COSV51522301;