ENST00000524085.2:n.299-13911_299-13910delGT

Variant names:

• chr8-81484005-GGT-G
• rs3834363
• ENST00000524085.2:n.299-13911_299-13910delGT

Variant summary

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

The ENST00000524085.2(ENSG00000253374):​n.299-13911_299-13910delGT variant causes a intron change involving the alteration of a non-conserved nucleotide. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.36 (10422 hom., cov: 0)
• Consequence: ENSG00000253374 ENST00000524085.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.574
• Publications: 3 publications found

Genes affected

ENSG00000253374 (HGNC:):

ACMG classification

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

• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.724 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000524085.2. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

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

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000253374	ENST00000524085.2	TSL:5	n.299-13911_299-13910delGT		intron	N/A
	ENSG00000253374	ENST00000832857.1		n.327-37701_327-37700delGT		intron	N/A
	ENSG00000253374	ENST00000832858.1		n.309-37701_309-37700delGT		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.355 AC: 52872 AN: 149048 Hom.: 10394 Cov.: 0

Gnomad AFR AF: 0.526

Gnomad AMI AF: 0.105

Gnomad AMR AF: 0.335

Gnomad ASJ AF: 0.271

Gnomad EAS AF: 0.744

Gnomad SAS AF: 0.298

Gnomad FIN AF: 0.199

Gnomad MID AF: 0.282

Gnomad NFE AF: 0.269

Gnomad OTH AF: 0.342

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

GnomAD4 genome AF: 0.355 AC: 52954 AN: 149158 Hom.: 10422 Cov.: 0 AF XY: 0.352 AC XY: 25725 AN XY: 73028

African (AFR) AF: 0.526 AC: 20439 AN: 38836

American (AMR) AF: 0.335 AC: 5061 AN: 15124

Ashkenazi Jewish (ASJ) AF: 0.271 AC: 939 AN: 3470

East Asian (EAS) AF: 0.744 AC: 3832 AN: 5154

South Asian (SAS) AF: 0.299 AC: 1439 AN: 4812

European-Finnish (FIN) AF: 0.199 AC: 2110 AN: 10580

Middle Eastern (MID) AF: 0.272 AC: 79 AN: 290

European-Non Finnish (NFE) AF: 0.269 AC: 18245 AN: 67906

Other (OTH) AF: 0.344 AC: 714 AN: 2074

Alfa AF: 0.329 Hom.: 1130

Bravo AF: 0.392

Asia WGS AF: 0.506 AC: 1756 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
PhyloP100		0.57

Splicing

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

Other links and lift over

dbSNP: rs3834363; hg19: chr8-82396240;