ENST00000536009.1:n.69+7295T>C

Variant names:

• chr12-119251654-A-G
• rs4576883
• ENST00000536009.1:n.69+7295T>C

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000536009.1(ENSG00000256311):​n.69+7295T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.143 in 152,220 control chromosomes in the GnomAD database, including 1,668 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 (1668 hom., cov: 33)
• Consequence: ENSG00000256311 ENST00000536009.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.405

Genes affected

ENSG00000256311 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.248 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
ENSG00000256311	ENST00000536009.1	n.69+7295T>C		intron_variant	Intron 1 of 4	3

Frequencies

GnomAD3 genomes AF: 0.142 AC: 21669 AN: 152100 Hom.: 1661 Cov.: 33

Gnomad AFR AF: 0.191

Gnomad AMI AF: 0.0669

Gnomad AMR AF: 0.109

Gnomad ASJ AF: 0.161

Gnomad EAS AF: 0.0767

Gnomad SAS AF: 0.260

Gnomad FIN AF: 0.110

Gnomad MID AF: 0.259

Gnomad NFE AF: 0.122

Gnomad OTH AF: 0.144

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

GnomAD4 genome AF: 0.143 AC: 21696 AN: 152220 Hom.: 1668 Cov.: 33 AF XY: 0.141 AC XY: 10507 AN XY: 74416

Gnomad4 AFR AF: 0.191

Gnomad4 AMR AF: 0.109

Gnomad4 ASJ AF: 0.161

Gnomad4 EAS AF: 0.0767

Gnomad4 SAS AF: 0.260

Gnomad4 FIN AF: 0.110

Gnomad4 NFE AF: 0.122

Gnomad4 OTH AF: 0.147

Alfa AF: 0.128 Hom.: 1260

Bravo AF: 0.140

Asia WGS AF: 0.194 AC: 676 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.69
DANN	Benign	0.70

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4576883; hg19: chr12-119689459;