ENST00000513332.5:n.280-51097A>T

Variant names:

• chr4-136171235-T-A
• rs1451125
• ENST00000513332.5:n.280-51097A>T

Variant summary

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

The ENST00000513332.5(ENSG00000251567):​n.280-51097A>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.321 in 151,884 control chromosomes in the GnomAD database, including 7,882 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 0.32 (7882 hom., cov: 31)
• Consequence: ENSG00000251567 ENST00000513332.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.108
• Publications: 2 publications found

Genes affected

ENSG00000251567 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.44 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
ENSG00000251567	ENST00000513332.5	n.280-51097A>T		intron_variant	Intron 2 of 3	3

Frequencies

GnomAD3 genomes AF: 0.321 AC: 48651 AN: 151768 Hom.: 7873 Cov.: 31

Gnomad AFR AF: 0.310

Gnomad AMI AF: 0.255

Gnomad AMR AF: 0.341

Gnomad ASJ AF: 0.259

Gnomad EAS AF: 0.456

Gnomad SAS AF: 0.394

Gnomad FIN AF: 0.346

Gnomad MID AF: 0.203

Gnomad NFE AF: 0.308

Gnomad OTH AF: 0.314

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

GnomAD4 genome AF: 0.321 AC: 48683 AN: 151884 Hom.: 7882 Cov.: 31 AF XY: 0.324 AC XY: 24064 AN XY: 74242

African (AFR) AF: 0.310 AC: 12838 AN: 41406

American (AMR) AF: 0.341 AC: 5210 AN: 15262

Ashkenazi Jewish (ASJ) AF: 0.259 AC: 898 AN: 3466

East Asian (EAS) AF: 0.456 AC: 2338 AN: 5130

South Asian (SAS) AF: 0.393 AC: 1892 AN: 4816

European-Finnish (FIN) AF: 0.346 AC: 3651 AN: 10542

Middle Eastern (MID) AF: 0.197 AC: 58 AN: 294

European-Non Finnish (NFE) AF: 0.308 AC: 20896 AN: 67952

Other (OTH) AF: 0.318 AC: 670 AN: 2106

Alfa AF: 0.319 Hom.: 967

Bravo AF: 0.319

Asia WGS AF: 0.425 AC: 1481 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.58
DANN	Benign	0.39
PhyloP100		0.11

Splicing

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

Other links and lift over

dbSNP: rs1451125; hg19: chr4-137092390;