8-2817587-C-T

Variant names:

• chr8-2817587-C-T
• rs2924887
• ENST00000520024.1:n.369-1680C>T

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000520024.1(ENSG00000253853):​n.369-1680C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.422 in 152,024 control chromosomes in the GnomAD database, including 18,737 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 0.42 (18737 hom., cov: 32)
• Consequence: ENSG00000253853 ENST00000520024.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.30
• Publications: 2 publications found

Genes affected

ENSG00000253853 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.01).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.809 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105377785	NR_168441.1	n.662+12878C>T		intron_variant	Intron 2 of 11
LOC105377785	NR_168442.1	n.662+12878C>T		intron_variant	Intron 2 of 14
LOC105377785	NR_168443.1	n.662+12878C>T		intron_variant	Intron 2 of 8

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000253853	ENST00000520024.1	n.369-1680C>T		intron_variant	Intron 3 of 4	3
ENSG00000253853	ENST00000654515.1	n.655+12878C>T		intron_variant	Intron 2 of 5
ENSG00000253853	ENST00000662575.1	n.206-1680C>T		intron_variant	Intron 2 of 3

Frequencies

GnomAD3 genomes AF: 0.422 AC: 64051 AN: 151906 Hom.: 18675 Cov.: 32

Gnomad AFR AF: 0.816

Gnomad AMI AF: 0.258

Gnomad AMR AF: 0.480

Gnomad ASJ AF: 0.278

Gnomad EAS AF: 0.442

Gnomad SAS AF: 0.354

Gnomad FIN AF: 0.196

Gnomad MID AF: 0.405

Gnomad NFE AF: 0.218

Gnomad OTH AF: 0.382

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

GnomAD4 genome AF: 0.422 AC: 64179 AN: 152024 Hom.: 18737 Cov.: 32 AF XY: 0.423 AC XY: 31413 AN XY: 74288

African (AFR) AF: 0.817 AC: 33867 AN: 41466

American (AMR) AF: 0.481 AC: 7350 AN: 15296

Ashkenazi Jewish (ASJ) AF: 0.278 AC: 966 AN: 3472

East Asian (EAS) AF: 0.443 AC: 2276 AN: 5142

South Asian (SAS) AF: 0.352 AC: 1693 AN: 4810

European-Finnish (FIN) AF: 0.196 AC: 2071 AN: 10560

Middle Eastern (MID) AF: 0.408 AC: 120 AN: 294

European-Non Finnish (NFE) AF: 0.218 AC: 14790 AN: 67964

Other (OTH) AF: 0.384 AC: 811 AN: 2110

Alfa AF: 0.252 Hom.: 1113

Bravo AF: 0.462

Asia WGS AF: 0.401 AC: 1396 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.049
DANN	Benign	0.54
PhyloP100		-1.3

Splicing

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

Other links and lift over

dbSNP: rs2924887; hg19: chr8-2675109;