ENST00000520024.1:n.176+38038T>C

Variant names:

• chr8-2765531-T-C
• rs4602918
• ENST00000520024.1:n.176+38038T>C

Variant summary

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

The ENST00000520024.1(ENSG00000253853):​n.176+38038T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.452 in 151,994 control chromosomes in the GnomAD database, including 20,560 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 0.45 (20560 hom., cov: 33)
• Consequence: ENSG00000253853 ENST00000520024.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.152
• 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=-0.97).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.836 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000520024.1. 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
	LOC105377785	NR_168441.1		n.538+38038T>C		intron	N/A
	LOC105377785	NR_168442.1		n.538+38038T>C		intron	N/A
	LOC105377785	NR_168443.1		n.538+38038T>C		intron	N/A

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000253853	ENST00000520024.1	TSL:3	n.176+38038T>C		intron	N/A
	ENSG00000253853	ENST00000654515.1		n.531+38038T>C		intron	N/A
	ENSG00000253853	ENST00000670600.1		n.538+38038T>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.451 AC: 68551 AN: 151876 Hom.: 20504 Cov.: 33

Gnomad AFR AF: 0.843

Gnomad AMI AF: 0.323

Gnomad AMR AF: 0.509

Gnomad ASJ AF: 0.332

Gnomad EAS AF: 0.519

Gnomad SAS AF: 0.295

Gnomad FIN AF: 0.255

Gnomad MID AF: 0.430

Gnomad NFE AF: 0.246

Gnomad OTH AF: 0.415

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

GnomAD4 genome AF: 0.452 AC: 68665 AN: 151994 Hom.: 20560 Cov.: 33 AF XY: 0.454 AC XY: 33706 AN XY: 74320

African (AFR) AF: 0.844 AC: 34941 AN: 41416

American (AMR) AF: 0.510 AC: 7786 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.332 AC: 1154 AN: 3472

East Asian (EAS) AF: 0.519 AC: 2663 AN: 5132

South Asian (SAS) AF: 0.293 AC: 1415 AN: 4822

European-Finnish (FIN) AF: 0.255 AC: 2691 AN: 10572

Middle Eastern (MID) AF: 0.432 AC: 127 AN: 294

European-Non Finnish (NFE) AF: 0.246 AC: 16713 AN: 67986

Other (OTH) AF: 0.417 AC: 880 AN: 2110

Alfa AF: 0.376 Hom.: 1942

Bravo AF: 0.492

Asia WGS AF: 0.437 AC: 1517 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	0.63
DANN	Benign	0.51
PhyloP100		-0.15

Splicing

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

Other links and lift over

dbSNP: rs4602918; hg19: chr8-2623069;