13-52208449-A-G

Variant names:

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

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 4 publications found

Genes affected

ENSG00000217576 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000451298.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000217576	ENST00000451298.1	TSL:2	n.1229+14790T>C		intron	N/A
	ENSG00000217576	ENST00000832956.1		n.446-18535T>C		intron	N/A
	ENSG00000217576	ENST00000832957.1		n.236-18535T>C		intron	N/A

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

African (AFR) AF: 0.960 AC: 39835 AN: 41502

American (AMR) AF: 0.961 AC: 14691 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.909 AC: 3154 AN: 3470

East Asian (EAS) AF: 0.999 AC: 5151 AN: 5154

South Asian (SAS) AF: 0.947 AC: 4555 AN: 4812

European-Finnish (FIN) AF: 0.938 AC: 9932 AN: 10588

Middle Eastern (MID) AF: 0.949 AC: 279 AN: 294

European-Non Finnish (NFE) AF: 0.923 AC: 62776 AN: 68002

Other (OTH) AF: 0.939 AC: 1979 AN: 2108

Alfa AF: 0.933 Hom.: 49774

Bravo AF: 0.945

Asia WGS AF: 0.954 AC: 3316 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	2.9
DANN	Benign	0.41
PhyloP100		0.090

Splicing

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

Other links and lift over

dbSNP: rs2094354; hg19: chr13-52782584;