ENST00000520024.1:n.176+11085G>T

Variant names:

• chr8-2738578-G-T
• rs17755518
• ENST00000520024.1:n.176+11085G>T

Variant summary

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

The ENST00000520024.1(ENSG00000253853):​n.176+11085G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.186 in 151,956 control chromosomes in the GnomAD database, including 3,307 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 0.19 (3307 hom., cov: 32)
• Consequence: ENSG00000253853 ENST00000520024.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.178
• Publications: 7 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=-0.92).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.256 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+11085G>T		intron	N/A
	LOC105377785	NR_168442.1		n.538+11085G>T		intron	N/A
	LOC105377785	NR_168443.1		n.538+11085G>T		intron	N/A

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000253853	ENST00000520024.1	TSL:3	n.176+11085G>T		intron	N/A
	ENSG00000253853	ENST00000654515.1		n.531+11085G>T		intron	N/A
	ENSG00000253853	ENST00000670600.1		n.538+11085G>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.187 AC: 28324 AN: 151840 Hom.: 3308 Cov.: 32

Gnomad AFR AF: 0.0553

Gnomad AMI AF: 0.236

Gnomad AMR AF: 0.158

Gnomad ASJ AF: 0.181

Gnomad EAS AF: 0.240

Gnomad SAS AF: 0.232

Gnomad FIN AF: 0.224

Gnomad MID AF: 0.133

Gnomad NFE AF: 0.259

Gnomad OTH AF: 0.200

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

GnomAD4 genome AF: 0.186 AC: 28317 AN: 151956 Hom.: 3307 Cov.: 32 AF XY: 0.184 AC XY: 13669 AN XY: 74292

African (AFR) AF: 0.0552 AC: 2290 AN: 41486

American (AMR) AF: 0.158 AC: 2415 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.181 AC: 625 AN: 3460

East Asian (EAS) AF: 0.239 AC: 1235 AN: 5168

South Asian (SAS) AF: 0.232 AC: 1118 AN: 4812

European-Finnish (FIN) AF: 0.224 AC: 2359 AN: 10540

Middle Eastern (MID) AF: 0.126 AC: 37 AN: 294

European-Non Finnish (NFE) AF: 0.259 AC: 17601 AN: 67902

Other (OTH) AF: 0.200 AC: 423 AN: 2112

Alfa AF: 0.227 Hom.: 11176

Bravo AF: 0.175

Asia WGS AF: 0.222 AC: 770 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	6.1
DANN	Benign	0.67
PhyloP100		-0.18

Splicing

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

Other links and lift over

dbSNP: rs17755518; hg19: chr8-2596106;