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).

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
ENSG00000303925	ENST00000798091.1	n.222-3008G>C		intron_variant	Intron 2 of 2
ENSG00000303925	ENST00000798092.1	n.116-3008G>C		intron_variant	Intron 1 of 1

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 v4.3

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

Other links and lift over

dbSNP: rs223692; hg19: chrX-88760726;