rs3834363

Variant names:

• chr8-81484005-GGT-G
• rs3834363
• ENST00000524085.2:n.299-13906_299-13905delTG

Variant summary

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

The ENST00000524085.2(ENSG00000253374):​n.299-13906_299-13905delTG 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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC101927118	XR_001745980.2	n.517+22037_517+22038delTG		intron_variant	Intron 1 of 8

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000253374	ENST00000524085.2	n.299-13906_299-13905delTG		intron_variant	Intron 2 of 3	5
ENSG00000253374	ENST00000832857.1	n.327-37696_327-37695delTG		intron_variant	Intron 2 of 9
ENSG00000253374	ENST00000832858.1	n.309-37696_309-37695delTG		intron_variant	Intron 2 of 9
ENSG00000253374	ENST00000832859.1	n.328-37696_328-37695delTG		intron_variant	Intron 2 of 5

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 v4.3

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;