ENST00000433835.3:c.432-2714C>T

Variant names:

• chr22-23892058-C-T
• rs738807
• ENST00000433835.3:c.432-2714C>T

Variant summary

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

The ENST00000433835.3(ENSG00000251357):​c.432-2714C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.14 in 152,194 control chromosomes in the GnomAD database, including 1,697 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 0.14 (1697 hom., cov: 33)
• Consequence: ENSG00000251357 ENST00000433835.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.188
• Publications: 15 publications found

Genes affected

ENSG00000251357 (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 (AMR) allele frequency at 95% confidence interval = 0.184 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
ENSG00000251357	ENST00000433835.3	c.432-2714C>T		intron_variant	Intron 4 of 5	5		ENSP00000400325.3
ENSG00000290199	ENST00000717616.1	n.213-592G>A		intron_variant	Intron 2 of 2

Frequencies

GnomAD3 genomes AF: 0.140 AC: 21359 AN: 152076 Hom.: 1692 Cov.: 33

Gnomad AFR AF: 0.119

Gnomad AMI AF: 0.0899

Gnomad AMR AF: 0.189

Gnomad ASJ AF: 0.0464

Gnomad EAS AF: 0.185

Gnomad SAS AF: 0.131

Gnomad FIN AF: 0.216

Gnomad MID AF: 0.101

Gnomad NFE AF: 0.134

Gnomad OTH AF: 0.120

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

GnomAD4 genome AF: 0.140 AC: 21379 AN: 152194 Hom.: 1697 Cov.: 33 AF XY: 0.146 AC XY: 10838 AN XY: 74404

African (AFR) AF: 0.119 AC: 4956 AN: 41524

American (AMR) AF: 0.190 AC: 2905 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.0464 AC: 161 AN: 3470

East Asian (EAS) AF: 0.185 AC: 956 AN: 5178

South Asian (SAS) AF: 0.132 AC: 637 AN: 4824

European-Finnish (FIN) AF: 0.216 AC: 2284 AN: 10590

Middle Eastern (MID) AF: 0.0952 AC: 28 AN: 294

European-Non Finnish (NFE) AF: 0.134 AC: 9121 AN: 68004

Other (OTH) AF: 0.118 AC: 249 AN: 2114

Alfa AF: 0.133 Hom.: 1154

Bravo AF: 0.136

Asia WGS AF: 0.177 AC: 617 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	1.6
DANN	Benign	0.48
PhyloP100		-0.19

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

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

Other links and lift over

dbSNP: rs738807; hg19: chr22-24234245;