ENST00000432386.1:n.76+594T>A

Variant names:

• chr1-151995200-T-A
• rs4845720
• ENST00000432386.1:n.76+594T>A

Variant summary

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

The ENST00000432386.1(ENSG00000229021):​n.76+594T>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0411 in 152,266 control chromosomes in the GnomAD database, including 163 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 0.041 (163 hom., cov: 30)
• Consequence: ENSG00000229021 ENST00000432386.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.512
• Publications: 2 publications found

Genes affected

ENSG00000229021 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.78).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.0706 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
ENSG00000229021	ENST00000432386.1	n.76+594T>A		intron_variant	Intron 1 of 12	2

Frequencies

GnomAD3 genomes AF: 0.0410 AC: 6242 AN: 152148 Hom.: 160 Cov.: 30

Gnomad AFR AF: 0.0727

Gnomad AMI AF: 0.0571

Gnomad AMR AF: 0.0256

Gnomad ASJ AF: 0.00606

Gnomad EAS AF: 0.0273

Gnomad SAS AF: 0.0130

Gnomad FIN AF: 0.0226

Gnomad MID AF: 0.0285

Gnomad NFE AF: 0.0329

Gnomad OTH AF: 0.0349

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

GnomAD4 genome AF: 0.0411 AC: 6252 AN: 152266 Hom.: 163 Cov.: 30 AF XY: 0.0393 AC XY: 2923 AN XY: 74450

African (AFR) AF: 0.0728 AC: 3024 AN: 41546

American (AMR) AF: 0.0256 AC: 391 AN: 15302

Ashkenazi Jewish (ASJ) AF: 0.00606 AC: 21 AN: 3466

East Asian (EAS) AF: 0.0272 AC: 141 AN: 5180

South Asian (SAS) AF: 0.0129 AC: 62 AN: 4824

European-Finnish (FIN) AF: 0.0226 AC: 240 AN: 10610

Middle Eastern (MID) AF: 0.0272 AC: 8 AN: 294

European-Non Finnish (NFE) AF: 0.0329 AC: 2240 AN: 68022

Other (OTH) AF: 0.0346 AC: 73 AN: 2112

Alfa AF: 0.0404 Hom.: 13

Bravo AF: 0.0424

Asia WGS AF: 0.0480 AC: 166 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.78
CADD	Benign	7.7
DANN	Benign	0.81
PhyloP100		-0.51

Splicing

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

Other links and lift over

dbSNP: rs4845720; hg19: chr1-151967676;