X-89505727-C-G

Variant names:

• chrX-89505727-C-G
• rs223692
• ENST00000798091.1:n.222-3008G>C

Variant summary

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

The ENST00000798091.1(ENSG00000303925):​n.222-3008G>C 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 0.63 (17624 hom., 16477 hem., cov: 18)
  • Failed GnomAD Quality Control
• Consequence: ENSG00000303925 ENST00000798091.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.262
• Publications: 1 publications found

Genes affected

ENSG00000303925 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000798091.1. 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
	ENSG00000303925	ENST00000798091.1		n.222-3008G>C		intron	N/A
	ENSG00000303925	ENST00000798092.1		n.116-3008G>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.633 AC: 65577 AN: 103533 Hom.: 17629 Cov.: 18

Gnomad AFR AF: 0.276

Gnomad AMI AF: 0.868

Gnomad AMR AF: 0.664

Gnomad ASJ AF: 0.742

Gnomad EAS AF: 0.756

Gnomad SAS AF: 0.567

Gnomad FIN AF: 0.811

Gnomad MID AF: 0.743

Gnomad NFE AF: 0.798

Gnomad OTH AF: 0.668

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: 0.633 AC: 65565 AN: 103581 Hom.: 17624 Cov.: 18 AF XY: 0.624 AC XY: 16477 AN XY: 26399

African (AFR) AF: 0.275 AC: 7884 AN: 28642

American (AMR) AF: 0.664 AC: 6254 AN: 9422

Ashkenazi Jewish (ASJ) AF: 0.742 AC: 1885 AN: 2539

East Asian (EAS) AF: 0.756 AC: 2418 AN: 3198

South Asian (SAS) AF: 0.566 AC: 1182 AN: 2088

European-Finnish (FIN) AF: 0.811 AC: 3979 AN: 4905

Middle Eastern (MID) AF: 0.726 AC: 143 AN: 197

European-Non Finnish (NFE) AF: 0.798 AC: 40342 AN: 50572

Other (OTH) AF: 0.669 AC: 920 AN: 1375

Alfa AF: 0.480 Hom.: 1589

Bravo AF: 0.620

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	2.9
DANN	Benign	0.56
PhyloP100		0.26

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: rs223692;

hg19: chrX-88760726;