chrX-138200029-G-C

Variant names:

• chrX-138200029-G-C
• rs609951

Variant summary

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

The variant allele was found at a frequency of 0.0000219 in 91,422 control chromosomes in the GnomAD database, with no homozygous occurrence. There are no hemizygote samples in GnomAD. 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 0.000022 (0 hom., 0 hem., cov: 23)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.249
• Publications: 0 publications found

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

 

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
There are no transcript annotations for this variant.

Frequencies

GnomAD3 genomes AF: 0.0000219 AC: 2 AN: 91422 Hom.: 0 Cov.: 23

Gnomad AFR AF: 0.00

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.00

Gnomad ASJ AF: 0.00

Gnomad EAS AF: 0.000613

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: 0.0000219 AC: 2 AN: 91422 Hom.: 0 Cov.: 23 AF XY: 0.00 AC XY: 0 AN XY: 20106

African (AFR) AF: 0.00 AC: 0 AN: 23411

American (AMR) AF: 0.00 AC: 0 AN: 8173

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 2320

East Asian (EAS) AF: 0.000613 AC: 2 AN: 3261

South Asian (SAS) AF: 0.00 AC: 0 AN: 1647

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 4730

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 207

European-Non Finnish (NFE) AF: 0.00 AC: 0 AN: 45841

Other (OTH) AF: 0.00 AC: 0 AN: 1242

Alfa AF: 0.00 Hom.: 956

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	2.3
DANN	Benign	0.33
PhyloP100		0.25

Splicing

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

Other links and lift over

dbSNP: rs609951; hg19: chrX-137282188;