ENST00000451298.1:n.1229+14790T>C

Variant names:

• chr13-52208449-A-G
• rs2094354
• ENST00000451298.1:n.1229+14790T>C

Variant summary

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

The ENST00000451298.1(ENSG00000217576):​n.1229+14790T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.941 in 152,126 control chromosomes in the GnomAD database, including 67,448 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 0.94 (67448 hom., cov: 29)
• Consequence: ENSG00000217576 ENST00000451298.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0900

Genes affected

ENSG00000217576 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.977 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
ENSG00000217576	ENST00000451298.1	n.1229+14790T>C		intron_variant	Intron 14 of 21	2

Frequencies

GnomAD3 genomes AF: 0.941 AC: 143106 AN: 152008 Hom.: 67397 Cov.: 29

Gnomad AFR AF: 0.960

Gnomad AMI AF: 0.947

Gnomad AMR AF: 0.961

Gnomad ASJ AF: 0.909

Gnomad EAS AF: 0.999

Gnomad SAS AF: 0.947

Gnomad FIN AF: 0.938

Gnomad MID AF: 0.946

Gnomad NFE AF: 0.923

Gnomad OTH AF: 0.940

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

GnomAD4 genome AF: 0.941 AC: 143216 AN: 152126 Hom.: 67448 Cov.: 29 AF XY: 0.943 AC XY: 70144 AN XY: 74364

Gnomad4 AFR AF: 0.960

Gnomad4 AMR AF: 0.961

Gnomad4 ASJ AF: 0.909

Gnomad4 EAS AF: 0.999

Gnomad4 SAS AF: 0.947

Gnomad4 FIN AF: 0.938

Gnomad4 NFE AF: 0.923

Gnomad4 OTH AF: 0.939

Alfa AF: 0.926 Hom.: 29426

Bravo AF: 0.945

Asia WGS AF: 0.954 AC: 3316 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	2.9
DANN	Benign	0.41

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2094354; hg19: chr13-52782584;