chrX-94590840-C-T

Variant names:

• chrX-94590840-C-T
• rs5950049
• ENST00000765941.1:n.99+9267G>A

Variant summary

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

The ENST00000765941.1(ENSG00000299734):​n.99+9267G>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 0.64 (16972 hom., 20179 hem., cov: 23)
  • Failed GnomAD Quality Control
• Consequence: ENSG00000299734 ENST00000765941.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.799
• Publications: 1 publications found

Genes affected

ENSG00000299734 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000765941.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

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

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000299734	ENST00000765941.1		n.99+9267G>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.636 AC: 70105 AN: 110254 Hom.: 16980 Cov.: 23

Gnomad AFR AF: 0.599

Gnomad AMI AF: 0.726

Gnomad AMR AF: 0.424

Gnomad ASJ AF: 0.811

Gnomad EAS AF: 0.0170

Gnomad SAS AF: 0.378

Gnomad FIN AF: 0.760

Gnomad MID AF: 0.668

Gnomad NFE AF: 0.730

Gnomad OTH AF: 0.626

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: 0.636 AC: 70109 AN: 110310 Hom.: 16972 Cov.: 23 AF XY: 0.619 AC XY: 20179 AN XY: 32580

African (AFR) AF: 0.598 AC: 18099 AN: 30265

American (AMR) AF: 0.424 AC: 4405 AN: 10396

Ashkenazi Jewish (ASJ) AF: 0.811 AC: 2139 AN: 2637

East Asian (EAS) AF: 0.0171 AC: 60 AN: 3514

South Asian (SAS) AF: 0.380 AC: 995 AN: 2620

European-Finnish (FIN) AF: 0.760 AC: 4342 AN: 5712

Middle Eastern (MID) AF: 0.675 AC: 141 AN: 209

European-Non Finnish (NFE) AF: 0.730 AC: 38500 AN: 52766

Other (OTH) AF: 0.618 AC: 932 AN: 1508

Alfa AF: 0.686 Hom.: 20097

Bravo AF: 0.606

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	2.8
DANN	Benign	0.37
PhyloP100		0.80

Splicing

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

Other links and lift over

dbSNP: rs5950049; hg19: chrX-93845839;