chrX-120692753-G-T

Variant names:

• chrX-120692753-G-T
• rs1991961
• ENST00000719513.1:n.248-27125C>A

Variant summary

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

The ENST00000719513.1(ENSG00000293858):​n.248-27125C>A 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 (16224 hom., 20398 hem., cov: 22)
  • Failed GnomAD Quality Control
• Consequence: ENSG00000293858 ENST00000719513.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.208
• Publications: 3 publications found

Genes affected

ENSG00000293858 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000719513.1. 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
	ENSG00000293858	ENST00000719513.1		n.248-27125C>A		intron	N/A
	ENSG00000293858	ENST00000719514.1		n.139-22394C>A		intron	N/A
	ENSG00000293881	ENST00000719606.1		n.279+23896G>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.645 AC: 70634 AN: 109480 Hom.: 16223 Cov.: 22

Gnomad AFR AF: 0.665

Gnomad AMI AF: 0.511

Gnomad AMR AF: 0.597

Gnomad ASJ AF: 0.670

Gnomad EAS AF: 0.700

Gnomad SAS AF: 0.617

Gnomad FIN AF: 0.615

Gnomad MID AF: 0.624

Gnomad NFE AF: 0.645

Gnomad OTH AF: 0.632

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: 0.645 AC: 70679 AN: 109527 Hom.: 16224 Cov.: 22 AF XY: 0.640 AC XY: 20398 AN XY: 31847

African (AFR) AF: 0.665 AC: 19983 AN: 30031

American (AMR) AF: 0.596 AC: 6121 AN: 10271

Ashkenazi Jewish (ASJ) AF: 0.670 AC: 1764 AN: 2632

East Asian (EAS) AF: 0.700 AC: 2426 AN: 3467

South Asian (SAS) AF: 0.616 AC: 1577 AN: 2559

European-Finnish (FIN) AF: 0.615 AC: 3407 AN: 5542

Middle Eastern (MID) AF: 0.624 AC: 131 AN: 210

European-Non Finnish (NFE) AF: 0.645 AC: 33985 AN: 52661

Other (OTH) AF: 0.634 AC: 949 AN: 1496

Alfa AF: 0.638 Hom.: 78416

Bravo AF: 0.644

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	2.9
DANN	Benign	0.50
PhyloP100		0.21

Splicing

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

Other links and lift over

dbSNP: rs1991961; hg19: chrX-119826608;