5-158290898-C-A

Variant names:

• chr5-158290898-C-A
• rs2172745
• ENST00000809626.1:n.181-26467C>A

Variant summary

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

The ENST00000809626.1(ENSG00000253673):​n.181-26467C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.226 in 152,158 control chromosomes in the GnomAD database, including 4,071 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 0.23 (4071 hom., cov: 33)
• Consequence: ENSG00000253673 ENST00000809626.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.201
• Publications: 4 publications found

Genes affected

ENSG00000253673 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.65).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.253 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
ENSG00000253673	ENST00000809626.1	n.181-26467C>A		intron_variant	Intron 2 of 4

Frequencies

GnomAD3 genomes AF: 0.226 AC: 34383 AN: 152040 Hom.: 4073 Cov.: 33

Gnomad AFR AF: 0.190

Gnomad AMI AF: 0.197

Gnomad AMR AF: 0.197

Gnomad ASJ AF: 0.243

Gnomad EAS AF: 0.0772

Gnomad SAS AF: 0.263

Gnomad FIN AF: 0.260

Gnomad MID AF: 0.363

Gnomad NFE AF: 0.256

Gnomad OTH AF: 0.255

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

GnomAD4 genome AF: 0.226 AC: 34389 AN: 152158 Hom.: 4071 Cov.: 33 AF XY: 0.227 AC XY: 16903 AN XY: 74386

African (AFR) AF: 0.190 AC: 7868 AN: 41508

American (AMR) AF: 0.197 AC: 3011 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.243 AC: 844 AN: 3472

East Asian (EAS) AF: 0.0774 AC: 401 AN: 5180

South Asian (SAS) AF: 0.263 AC: 1269 AN: 4826

European-Finnish (FIN) AF: 0.260 AC: 2748 AN: 10578

Middle Eastern (MID) AF: 0.353 AC: 103 AN: 292

European-Non Finnish (NFE) AF: 0.256 AC: 17420 AN: 67994

Other (OTH) AF: 0.258 AC: 545 AN: 2112

Alfa AF: 0.242 Hom.: 7636

Bravo AF: 0.216

Asia WGS AF: 0.205 AC: 710 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.65
CADD	Benign	12
DANN	Benign	0.81
PhyloP100		-0.20

Splicing

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

Other links and lift over

dbSNP: rs2172745; hg19: chr5-157717906; COSMIC: COSV60221007;