ENST00000687547.2:n.2252T>G

Variant names:

• chrX-122479066-T-G
• rs7881297
• ENST00000687547.2:n.2252T>G

Variant summary

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

The ENST00000687547.2(ENSG00000287776):​n.2252T>G variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.181 in 111,305 control chromosomes in the GnomAD database, including 3,581 homozygotes. There are 5,570 hemizygotes in GnomAD. 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 0.18 (3581 hom., 5570 hem., cov: 23)
• Consequence: ENSG00000287776 ENST00000687547.2 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.507
• Publications: 2 publications found

Genes affected

ENSG00000287776 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.05).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.541 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
ENSG00000287776	ENST00000687547.2	n.2252T>G		non_coding_transcript_exon_variant	Exon 3 of 3
ENSG00000287776	ENST00000687758.2	n.2126T>G		non_coding_transcript_exon_variant	Exon 2 of 2

Frequencies

GnomAD3 genomes AF: 0.181 AC: 20114 AN: 111254 Hom.: 3579 Cov.: 23

Gnomad AFR AF: 0.548

Gnomad AMI AF: 0.00580

Gnomad AMR AF: 0.181

Gnomad ASJ AF: 0.0211

Gnomad EAS AF: 0.152

Gnomad SAS AF: 0.0763

Gnomad FIN AF: 0.00149

Gnomad MID AF: 0.0675

Gnomad NFE AF: 0.0102

Gnomad OTH AF: 0.182

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

GnomAD4 genome AF: 0.181 AC: 20158 AN: 111305 Hom.: 3581 Cov.: 23 AF XY: 0.166 AC XY: 5570 AN XY: 33557

African (AFR) AF: 0.548 AC: 16628 AN: 30338

American (AMR) AF: 0.181 AC: 1896 AN: 10448

Ashkenazi Jewish (ASJ) AF: 0.0211 AC: 56 AN: 2648

East Asian (EAS) AF: 0.152 AC: 534 AN: 3508

South Asian (SAS) AF: 0.0762 AC: 204 AN: 2678

European-Finnish (FIN) AF: 0.00149 AC: 9 AN: 6047

Middle Eastern (MID) AF: 0.0645 AC: 14 AN: 217

European-Non Finnish (NFE) AF: 0.0102 AC: 541 AN: 53220

Other (OTH) AF: 0.180 AC: 272 AN: 1511

Alfa AF: 0.0823 Hom.: 6534

Bravo AF: 0.217

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.1
CADD	Benign	0.43
DANN	Benign	0.40
PhyloP100		-0.51

Splicing

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

Other links and lift over

dbSNP: rs7881297; hg19: chrX-121612919;