1-25076389-A-T

Variant names:

• chr1-25076389-A-T
• rs372151
• ENST00000424084.1:n.360+27464T>A

Variant summary

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

The ENST00000424084.1(ENSG00000233755):​n.360+27464T>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.561 in 152,058 control chromosomes in the GnomAD database, including 25,426 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 0.56 (25426 hom., cov: 32)
• Consequence: ENSG00000233755 ENST00000424084.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.352
• Publications: 2 publications found

Genes affected

ENSG00000233755 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.77 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
ENSG00000233755	ENST00000424084.1	n.360+27464T>A		intron_variant	Intron 2 of 2	3

Frequencies

GnomAD3 genomes AF: 0.561 AC: 85179 AN: 151940 Hom.: 25385 Cov.: 32

Gnomad AFR AF: 0.777

Gnomad AMI AF: 0.536

Gnomad AMR AF: 0.445

Gnomad ASJ AF: 0.544

Gnomad EAS AF: 0.430

Gnomad SAS AF: 0.457

Gnomad FIN AF: 0.398

Gnomad MID AF: 0.611

Gnomad NFE AF: 0.498

Gnomad OTH AF: 0.578

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

GnomAD4 genome AF: 0.561 AC: 85273 AN: 152058 Hom.: 25426 Cov.: 32 AF XY: 0.551 AC XY: 40925 AN XY: 74330

African (AFR) AF: 0.778 AC: 32268 AN: 41500

American (AMR) AF: 0.444 AC: 6778 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.544 AC: 1884 AN: 3466

East Asian (EAS) AF: 0.430 AC: 2227 AN: 5176

South Asian (SAS) AF: 0.456 AC: 2195 AN: 4812

European-Finnish (FIN) AF: 0.398 AC: 4203 AN: 10548

Middle Eastern (MID) AF: 0.616 AC: 180 AN: 292

European-Non Finnish (NFE) AF: 0.498 AC: 33825 AN: 67966

Other (OTH) AF: 0.579 AC: 1225 AN: 2114

Alfa AF: 0.520 Hom.: 2709

Bravo AF: 0.573

Asia WGS AF: 0.516 AC: 1796 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	3.7
DANN	Benign	0.68
PhyloP100		0.35

Splicing

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

Other links and lift over

dbSNP: rs372151; hg19: chr1-25402880;