ENST00000425894.2:n.182+28439C>T

Variant names:

• chr3-5663365-C-T
• rs11710433
• ENST00000425894.2:n.182+28439C>T

Variant summary

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

The ENST00000425894.2(ENSG00000229642):​n.182+28439C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.647 in 151,934 control chromosomes in the GnomAD database, including 33,222 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 0.65 (33222 hom., cov: 32)
• Consequence: ENSG00000229642 ENST00000425894.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0890
• Publications: 5 publications found

Genes affected

ENSG00000229642 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.844 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
ENSG00000229642	ENST00000425894.2	n.182+28439C>T		intron_variant	Intron 1 of 8	3
ENSG00000229642	ENST00000779001.1	n.103+2413C>T		intron_variant	Intron 1 of 7
ENSG00000229642	ENST00000779002.1	n.123+28439C>T		intron_variant	Intron 1 of 7

Frequencies

GnomAD3 genomes AF: 0.646 AC: 98109 AN: 151816 Hom.: 33153 Cov.: 32

Gnomad AFR AF: 0.851

Gnomad AMI AF: 0.387

Gnomad AMR AF: 0.596

Gnomad ASJ AF: 0.484

Gnomad EAS AF: 0.806

Gnomad SAS AF: 0.633

Gnomad FIN AF: 0.588

Gnomad MID AF: 0.453

Gnomad NFE AF: 0.545

Gnomad OTH AF: 0.586

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

GnomAD4 genome AF: 0.647 AC: 98240 AN: 151934 Hom.: 33222 Cov.: 32 AF XY: 0.647 AC XY: 48036 AN XY: 74214

African (AFR) AF: 0.852 AC: 35330 AN: 41474

American (AMR) AF: 0.595 AC: 9076 AN: 15244

Ashkenazi Jewish (ASJ) AF: 0.484 AC: 1678 AN: 3468

East Asian (EAS) AF: 0.806 AC: 4153 AN: 5154

South Asian (SAS) AF: 0.633 AC: 3043 AN: 4806

European-Finnish (FIN) AF: 0.588 AC: 6191 AN: 10536

Middle Eastern (MID) AF: 0.456 AC: 134 AN: 294

European-Non Finnish (NFE) AF: 0.545 AC: 37034 AN: 67936

Other (OTH) AF: 0.591 AC: 1248 AN: 2110

Alfa AF: 0.629 Hom.: 22018

Bravo AF: 0.657

Asia WGS AF: 0.733 AC: 2539 AN: 3464

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	4.4
DANN	Benign	0.43
PhyloP100		0.089

Splicing

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

Other links and lift over

dbSNP: rs11710433; hg19: chr3-5705052;