ENST00000520024.1:n.369-5279C>T

Variant names:

• chr8-2813988-C-T
• rs7010867
• ENST00000520024.1:n.369-5279C>T

Variant summary

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

The ENST00000520024.1(ENSG00000253853):​n.369-5279C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.39 in 152,096 control chromosomes in the GnomAD database, including 14,392 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 0.39 (14392 hom., cov: 33)
• Consequence: ENSG00000253853 ENST00000520024.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.326
• Publications: 3 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=-0.89).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.66 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105377785	NR_168441.1	n.662+9279C>T		intron_variant	Intron 2 of 11
LOC105377785	NR_168442.1	n.662+9279C>T		intron_variant	Intron 2 of 14
LOC105377785	NR_168443.1	n.662+9279C>T		intron_variant	Intron 2 of 8

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000253853	ENST00000520024.1	n.369-5279C>T		intron_variant	Intron 3 of 4	3
ENSG00000253853	ENST00000654515.1	n.655+9279C>T		intron_variant	Intron 2 of 5
ENSG00000253853	ENST00000662575.1	n.206-5279C>T		intron_variant	Intron 2 of 3

Frequencies

GnomAD3 genomes AF: 0.390 AC: 59222 AN: 151978 Hom.: 14353 Cov.: 33

Gnomad AFR AF: 0.667

Gnomad AMI AF: 0.249

Gnomad AMR AF: 0.475

Gnomad ASJ AF: 0.294

Gnomad EAS AF: 0.463

Gnomad SAS AF: 0.365

Gnomad FIN AF: 0.217

Gnomad MID AF: 0.380

Gnomad NFE AF: 0.233

Gnomad OTH AF: 0.365

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

GnomAD4 genome AF: 0.390 AC: 59319 AN: 152096 Hom.: 14392 Cov.: 33 AF XY: 0.391 AC XY: 29075 AN XY: 74322

African (AFR) AF: 0.667 AC: 27675 AN: 41506

American (AMR) AF: 0.476 AC: 7272 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.294 AC: 1019 AN: 3468

East Asian (EAS) AF: 0.463 AC: 2385 AN: 5148

South Asian (SAS) AF: 0.364 AC: 1752 AN: 4818

European-Finnish (FIN) AF: 0.217 AC: 2293 AN: 10576

Middle Eastern (MID) AF: 0.381 AC: 112 AN: 294

European-Non Finnish (NFE) AF: 0.233 AC: 15808 AN: 67978

Other (OTH) AF: 0.367 AC: 776 AN: 2112

Alfa AF: 0.299 Hom.: 25321

Bravo AF: 0.423

Asia WGS AF: 0.402 AC: 1400 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	1.7
DANN	Benign	0.30
PhyloP100		-0.33

Splicing

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

Other links and lift over

dbSNP: rs7010867; hg19: chr8-2671510;