ENST00000739587.1:n.167-5275T>G

Variant names:

• chr9-86626862-T-G
• rs952834
• ENST00000739587.1:n.167-5275T>G

Variant summary

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

The ENST00000739587.1(ENSG00000232211):​n.167-5275T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.562 in 152,122 control chromosomes in the GnomAD database, including 24,290 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 0.56 (24290 hom., cov: 33)
• Consequence: ENSG00000232211 ENST00000739587.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.31
• Publications: 3 publications found

Genes affected

ENSG00000232211 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.585 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
ENSG00000232211	ENST00000739587.1	n.167-5275T>G		intron_variant	Intron 1 of 2
ENSG00000232211	ENST00000739588.1	n.113-5275T>G		intron_variant	Intron 1 of 2
ENSG00000232211	ENST00000739589.1	n.99-5275T>G		intron_variant	Intron 2 of 3

Frequencies

GnomAD3 genomes AF: 0.563 AC: 85507 AN: 152004 Hom.: 24280 Cov.: 33

Gnomad AFR AF: 0.535

Gnomad AMI AF: 0.615

Gnomad AMR AF: 0.590

Gnomad ASJ AF: 0.507

Gnomad EAS AF: 0.374

Gnomad SAS AF: 0.484

Gnomad FIN AF: 0.596

Gnomad MID AF: 0.440

Gnomad NFE AF: 0.590

Gnomad OTH AF: 0.571

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

GnomAD4 genome AF: 0.562 AC: 85553 AN: 152122 Hom.: 24290 Cov.: 33 AF XY: 0.561 AC XY: 41690 AN XY: 74354

African (AFR) AF: 0.535 AC: 22200 AN: 41510

American (AMR) AF: 0.590 AC: 9018 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.507 AC: 1762 AN: 3472

East Asian (EAS) AF: 0.375 AC: 1937 AN: 5170

South Asian (SAS) AF: 0.484 AC: 2332 AN: 4820

European-Finnish (FIN) AF: 0.596 AC: 6300 AN: 10572

Middle Eastern (MID) AF: 0.435 AC: 128 AN: 294

European-Non Finnish (NFE) AF: 0.590 AC: 40107 AN: 67980

Other (OTH) AF: 0.572 AC: 1209 AN: 2112

Alfa AF: 0.514 Hom.: 2563

Bravo AF: 0.560

Asia WGS AF: 0.458 AC: 1596 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	6.5
DANN	Benign	0.46
PhyloP100		1.3

Splicing

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

Other links and lift over

dbSNP: rs952834; hg19: chr9-89241777;