X-140153333-C-T

Variant names:

• chrX-140153333-C-T
• rs677033
• ENST00000758029.1:n.253-5585C>T

Variant summary

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

The ENST00000758029.1(ENSG00000298798):​n.253-5585C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.391 in 110,784 control chromosomes in the GnomAD database, including 7,223 homozygotes. There are 12,990 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 0.39 (7223 hom., 12990 hem., cov: 23)
• Consequence: ENSG00000298798 ENST00000758029.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.700
• Publications: 0 publications found

Genes affected

ENSG00000298798 (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 (EAS) allele frequency at 95% confidence interval = 0.523 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
ENSG00000298798	ENST00000758029.1	n.253-5585C>T		intron_variant	Intron 2 of 2

Frequencies

GnomAD3 genomes AF: 0.391 AC: 43323 AN: 110733 Hom.: 7220 Cov.: 23

Gnomad AFR AF: 0.108

Gnomad AMI AF: 0.469

Gnomad AMR AF: 0.456

Gnomad ASJ AF: 0.459

Gnomad EAS AF: 0.544

Gnomad SAS AF: 0.438

Gnomad FIN AF: 0.507

Gnomad MID AF: 0.353

Gnomad NFE AF: 0.513

Gnomad OTH AF: 0.400

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

GnomAD4 genome AF: 0.391 AC: 43321 AN: 110784 Hom.: 7223 Cov.: 23 AF XY: 0.393 AC XY: 12990 AN XY: 33030

African (AFR) AF: 0.108 AC: 3309 AN: 30636

American (AMR) AF: 0.455 AC: 4729 AN: 10386

Ashkenazi Jewish (ASJ) AF: 0.459 AC: 1201 AN: 2614

East Asian (EAS) AF: 0.544 AC: 1882 AN: 3461

South Asian (SAS) AF: 0.438 AC: 1145 AN: 2617

European-Finnish (FIN) AF: 0.507 AC: 2954 AN: 5831

Middle Eastern (MID) AF: 0.355 AC: 76 AN: 214

European-Non Finnish (NFE) AF: 0.513 AC: 27097 AN: 52843

Other (OTH) AF: 0.406 AC: 612 AN: 1508

Alfa AF: 0.455 Hom.: 16804

Bravo AF: 0.376

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.67
PhyloP100		-0.70

Splicing

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

Other links and lift over

dbSNP: rs677033; hg19: chrX-139235492;