ENST00000520649.1:n.450-13738_450-13737dupTA

Variant names:

• chr8-86801493-C-CTA
• rs33974167
• ENST00000520649.1:n.450-13738_450-13737dupTA

Variant summary

Our verdict is Benign. The variant received -8 ACMG points: 0P and 8B. BA1

The ENST00000520649.1(ENSG00000253778):​n.450-13738_450-13737dupTA variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.252 in 151,756 control chromosomes in the GnomAD database, including 5,237 homozygotes. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.25 (5237 hom., cov: 22)
• Consequence: ENSG00000253778 ENST00000520649.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.719
• Publications: 2 publications found

Genes affected

ENSG00000253778 (HGNC:58258):

ACMG classification

Our verdict: Benign. The variant received -8 ACMG points.

• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.301 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
ENSG00000253778	ENST00000520649.1	n.450-13738_450-13737dupTA		intron_variant	Intron 3 of 5	3

Frequencies

GnomAD3 genomes AF: 0.252 AC: 38173 AN: 151638 Hom.: 5246 Cov.: 22

Gnomad AFR AF: 0.205

Gnomad AMI AF: 0.366

Gnomad AMR AF: 0.242

Gnomad ASJ AF: 0.315

Gnomad EAS AF: 0.00386

Gnomad SAS AF: 0.223

Gnomad FIN AF: 0.204

Gnomad MID AF: 0.436

Gnomad NFE AF: 0.304

Gnomad OTH AF: 0.288

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

GnomAD4 genome AF: 0.252 AC: 38176 AN: 151756 Hom.: 5237 Cov.: 22 AF XY: 0.246 AC XY: 18220 AN XY: 74162

African (AFR) AF: 0.205 AC: 8492 AN: 41452

American (AMR) AF: 0.241 AC: 3672 AN: 15212

Ashkenazi Jewish (ASJ) AF: 0.315 AC: 1091 AN: 3466

East Asian (EAS) AF: 0.00386 AC: 20 AN: 5176

South Asian (SAS) AF: 0.222 AC: 1068 AN: 4820

European-Finnish (FIN) AF: 0.204 AC: 2156 AN: 10564

Middle Eastern (MID) AF: 0.442 AC: 129 AN: 292

European-Non Finnish (NFE) AF: 0.304 AC: 20613 AN: 67758

Other (OTH) AF: 0.286 AC: 603 AN: 2110

Alfa AF: 0.269 Hom.: 695

Bravo AF: 0.251

Asia WGS AF: 0.122 AC: 426 AN: 3464

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
PhyloP100		-0.72

Splicing

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

Other links and lift over

dbSNP: rs33974167; hg19: chr8-87813721;