rs223692

Variant names:

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

Your query was ambiguous. Multiple possible variants found:

• chrX-89505727-C-A
• chrX-89505727-C-G
• chrX-89505727-C-T

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>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 0.0000097 (0 hom., 0 hem., cov: 18)
• 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=-0.95).

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>T		intron_variant	Intron 2 of 2
ENSG00000303925	ENST00000798092.1	n.116-3008G>T		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.00000965 AC: 1 AN: 103615 Hom.: 0 Cov.: 18

Gnomad AFR AF: 0.0000349

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.00

Gnomad ASJ AF: 0.00

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.00

Gnomad FIN AF: 0.00

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.00

Gnomad OTH AF: 0.00

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

GnomAD4 genome AF: 0.00000965 AC: 1 AN: 103615 Hom.: 0 Cov.: 18 AF XY: 0.00 AC XY: 0 AN XY: 26363

⚠️ The allele balance in gnomAD version 4 Genomes is significantly skewed from the expected value of 0.5.

African (AFR) AF: 0.0000349 AC: 1 AN: 28616

American (AMR) AF: 0.00 AC: 0 AN: 9421

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 2539

East Asian (EAS) AF: 0.00 AC: 0 AN: 3209

South Asian (SAS) AF: 0.00 AC: 0 AN: 2096

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 4907

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 219

European-Non Finnish (NFE) AF: 0.00 AC: 0 AN: 50605

Other (OTH) AF: 0.00 AC: 0 AN: 1360

⚠️ The allele balance in gnomAD version 4 Genomes is significantly skewed from the expected value of 0.5. (p-value = 0), which strongly suggests a high chance of mosaicism in these individuals.

Alfa AF: 0.00 Hom.: 1589

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	2.7
DANN	Benign	0.47
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;