chr8-19232269-T-TAAGG

Variant names:

• chr8-19232269-T-TAAGG
• rs2308072
• ENST00000517949.5:n.471+3191_471+3194dupCCTT

Variant summary

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

The ENST00000517949.5(ENSG00000253557):​n.471+3191_471+3194dupCCTT 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 0.49 (18393 hom., cov: 0)
• Consequence: ENSG00000253557 ENST00000517949.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.101
• Publications: 5 publications found

Genes affected

ENSG00000253557 (HGNC:):

ACMG classification

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

• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.578 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC100128993	NR_038919.1	n.504+3191_504+3194dupCCTT		intron_variant	Intron 2 of 4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000253557	ENST00000517949.5	n.471+3191_471+3194dupCCTT		intron_variant	Intron 2 of 3	3
ENSG00000253557	ENST00000518417.1	n.214+3191_214+3194dupCCTT		intron_variant	Intron 1 of 3	4
ENSG00000253557	ENST00000520920.5	n.410+3191_410+3194dupCCTT		intron_variant	Intron 3 of 4	4

Frequencies

GnomAD3 genomes AF: 0.487 AC: 73655 AN: 151324 Hom.: 18373 Cov.: 0

Gnomad AFR AF: 0.584

Gnomad AMI AF: 0.467

Gnomad AMR AF: 0.358

Gnomad ASJ AF: 0.402

Gnomad EAS AF: 0.385

Gnomad SAS AF: 0.290

Gnomad FIN AF: 0.514

Gnomad MID AF: 0.396

Gnomad NFE AF: 0.480

Gnomad OTH AF: 0.476

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

GnomAD4 genome AF: 0.487 AC: 73705 AN: 151442 Hom.: 18393 Cov.: 0 AF XY: 0.483 AC XY: 35726 AN XY: 73994

African (AFR) AF: 0.584 AC: 24056 AN: 41194

American (AMR) AF: 0.357 AC: 5440 AN: 15220

Ashkenazi Jewish (ASJ) AF: 0.402 AC: 1394 AN: 3468

East Asian (EAS) AF: 0.384 AC: 1976 AN: 5146

South Asian (SAS) AF: 0.290 AC: 1399 AN: 4826

European-Finnish (FIN) AF: 0.514 AC: 5378 AN: 10460

Middle Eastern (MID) AF: 0.388 AC: 114 AN: 294

European-Non Finnish (NFE) AF: 0.480 AC: 32541 AN: 67830

Other (OTH) AF: 0.469 AC: 987 AN: 2104

Alfa AF: 0.483 Hom.: 1932

Asia WGS AF: 0.354 AC: 1234 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
PhyloP100		0.10

Splicing

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

Other links and lift over

dbSNP: rs2308072; hg19: chr8-19089779;