X-121149018-C-T

Variant names:

• chrX-121149018-C-T
• rs2375486
• ENST00000651788.1:n.87-2593C>T

Variant summary

Our verdict is Likely benign. The variant received -4 ACMG points: 0P and 4B. BP4_Strong

The ENST00000651788.1(ENSG00000286163):​n.87-2593C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. 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 0.65 (17410 hom., 20082 hem., cov: 21)
  • Failed GnomAD Quality Control
• Consequence: ENSG00000286163 ENST00000651788.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.110
• Publications: 2 publications found

Genes affected

ENSG00000286163 (HGNC:):

ACMG classification

Our verdict: Likely_benign. The variant received -4 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.67).

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000651788.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000286163	ENST00000651788.1		n.87-2593C>T		intron	N/A
	ENSG00000286163	ENST00000768679.1		n.352-15041C>T		intron	N/A
	ENSG00000286163	ENST00000768680.1		n.271-2593C>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.647 AC: 70773 AN: 109342 Hom.: 17408 Cov.: 21

Gnomad AFR AF: 0.859

Gnomad AMI AF: 0.516

Gnomad AMR AF: 0.501

Gnomad ASJ AF: 0.561

Gnomad EAS AF: 0.304

Gnomad SAS AF: 0.459

Gnomad FIN AF: 0.628

Gnomad MID AF: 0.603

Gnomad NFE AF: 0.596

Gnomad OTH AF: 0.630

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

GnomAD4 genome Data not reliable, filtered out with message: InbreedingCoeff AF: 0.647 AC: 70817 AN: 109383 Hom.: 17410 Cov.: 21 AF XY: 0.634 AC XY: 20082 AN XY: 31687

African (AFR) AF: 0.859 AC: 25819 AN: 30045

American (AMR) AF: 0.500 AC: 5137 AN: 10274

Ashkenazi Jewish (ASJ) AF: 0.561 AC: 1472 AN: 2623

East Asian (EAS) AF: 0.304 AC: 1052 AN: 3466

South Asian (SAS) AF: 0.462 AC: 1193 AN: 2583

European-Finnish (FIN) AF: 0.628 AC: 3440 AN: 5475

Middle Eastern (MID) AF: 0.592 AC: 125 AN: 211

European-Non Finnish (NFE) AF: 0.596 AC: 31303 AN: 52554

Other (OTH) AF: 0.628 AC: 930 AN: 1481

Alfa AF: 0.605 Hom.: 39570

Bravo AF: 0.647

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.67
CADD	Benign	4.5
DANN	Benign	0.42
PhyloP100		0.11

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs2375486;

hg19: chrX-120282872;