ENST00000518722.2:n.260-5833G>T

Variant names:

• chr8-40395182-G-T
• rs11786458
• ENST00000518722.2:n.260-5833G>T

Variant summary

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

The ENST00000518722.2(ENSG00000253354):​n.260-5833G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.323 in 152,046 control chromosomes in the GnomAD database, including 9,084 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 0.32 (9084 hom., cov: 32)
• Consequence: ENSG00000253354 ENST00000518722.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0480
• Publications: 6 publications found

Genes affected

ENSG00000253354 (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 (EAS) allele frequency at 95% confidence interval = 0.686 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000253354	ENST00000518722.2	n.260-5833G>T		intron_variant	Intron 2 of 3	3
ENSG00000253354	ENST00000660702.1	n.282-5833G>T		intron_variant	Intron 2 of 3
ENSG00000289853	ENST00000701081.2	n.85+22527G>T		intron_variant	Intron 1 of 2

Frequencies

GnomAD3 genomes AF: 0.323 AC: 49115 AN: 151926 Hom.: 9073 Cov.: 32

Gnomad AFR AF: 0.180

Gnomad AMI AF: 0.131

Gnomad AMR AF: 0.427

Gnomad ASJ AF: 0.289

Gnomad EAS AF: 0.704

Gnomad SAS AF: 0.433

Gnomad FIN AF: 0.416

Gnomad MID AF: 0.253

Gnomad NFE AF: 0.341

Gnomad OTH AF: 0.304

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

GnomAD4 genome AF: 0.323 AC: 49153 AN: 152046 Hom.: 9084 Cov.: 32 AF XY: 0.333 AC XY: 24764 AN XY: 74306

African (AFR) AF: 0.180 AC: 7477 AN: 41500

American (AMR) AF: 0.427 AC: 6523 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.289 AC: 1002 AN: 3468

East Asian (EAS) AF: 0.705 AC: 3624 AN: 5140

South Asian (SAS) AF: 0.433 AC: 2084 AN: 4816

European-Finnish (FIN) AF: 0.416 AC: 4401 AN: 10568

Middle Eastern (MID) AF: 0.248 AC: 72 AN: 290

European-Non Finnish (NFE) AF: 0.341 AC: 23194 AN: 67966

Other (OTH) AF: 0.311 AC: 657 AN: 2112

Alfa AF: 0.339 Hom.: 28324

Bravo AF: 0.319

Asia WGS AF: 0.542 AC: 1880 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	1.4
DANN	Benign	0.51
PhyloP100		0.048

Splicing

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

Other links and lift over

dbSNP: rs11786458; hg19: chr8-40252701;