ENST00000432694.2:n.589+2066T>A

Variant names:

• chr1-173018590-T-A
• rs1033465
• ENST00000432694.2:n.589+2066T>A

Variant summary

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

The ENST00000432694.2(ENSG00000224000):​n.589+2066T>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.951 in 152,300 control chromosomes in the GnomAD database, including 69,002 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 0.95 (69002 hom., cov: 32)
• Consequence: ENSG00000224000 ENST00000432694.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -3.29
• Publications: 1 publications found

Genes affected

ENSG00000224000 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.02).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.979 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
ENSG00000224000	ENST00000432694.2	n.589+2066T>A		intron_variant	Intron 3 of 4	3
ENSG00000224000	ENST00000717048.1	n.324-45283T>A		intron_variant	Intron 2 of 2

Frequencies

GnomAD3 genomes AF: 0.951 AC: 144700 AN: 152182 Hom.: 68959 Cov.: 32

Gnomad AFR AF: 0.882

Gnomad AMI AF: 0.969

Gnomad AMR AF: 0.961

Gnomad ASJ AF: 0.963

Gnomad EAS AF: 0.966

Gnomad SAS AF: 0.911

Gnomad FIN AF: 0.989

Gnomad MID AF: 0.978

Gnomad NFE AF: 0.985

Gnomad OTH AF: 0.958

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

GnomAD4 genome AF: 0.951 AC: 144800 AN: 152300 Hom.: 69002 Cov.: 32 AF XY: 0.951 AC XY: 70776 AN XY: 74454

African (AFR) AF: 0.882 AC: 36616 AN: 41532

American (AMR) AF: 0.961 AC: 14705 AN: 15308

Ashkenazi Jewish (ASJ) AF: 0.963 AC: 3345 AN: 3472

East Asian (EAS) AF: 0.966 AC: 5003 AN: 5178

South Asian (SAS) AF: 0.911 AC: 4393 AN: 4822

European-Finnish (FIN) AF: 0.989 AC: 10509 AN: 10624

Middle Eastern (MID) AF: 0.976 AC: 287 AN: 294

European-Non Finnish (NFE) AF: 0.985 AC: 67041 AN: 68044

Other (OTH) AF: 0.954 AC: 2017 AN: 2114

Alfa AF: 0.967 Hom.: 8304

Bravo AF: 0.947

Asia WGS AF: 0.925 AC: 3217 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.081
DANN	Benign	0.64
PhyloP100		-3.3

Splicing

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

Other links and lift over

dbSNP: rs1033465; hg19: chr1-172987730;