X-139566088-C-T

Variant names:

• chrX-139566088-C-T
• rs17340148

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BS1 BS2

The variant allele was found at a frequency of 0.0288 in 111,810 control chromosomes in the GnomAD database, including 44 homozygotes. There are 938 hemizygotes 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 0.029 (44 hom., 938 hem., cov: 22)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.58
• Publications: 0 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BS1: Variant frequency is greater than expected in population sas. GnomAd4 allele frequency = 0.0288 (3217/111810) while in subpopulation SAS AF = 0.0507 (134/2643). AF 95% confidence interval is 0.0437. There are 44 homozygotes in GnomAd4. There are 938 alleles in the male GnomAd4 subpopulation. Median coverage is 22. This position passed quality control check.
• BS2: High Homozygotes in GnomAd4 at 44 gene

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: 0.0288 AC: 3219 AN: 111757 Hom.: 44 Cov.: 22

Gnomad AFR AF: 0.00566

Gnomad AMI AF: 0.109

Gnomad AMR AF: 0.0126

Gnomad ASJ AF: 0.00604

Gnomad EAS AF: 0.0135

Gnomad SAS AF: 0.0505

Gnomad FIN AF: 0.0499

Gnomad MID AF: 0.0127

Gnomad NFE AF: 0.0432

Gnomad OTH AF: 0.0280

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

GnomAD4 genome AF: 0.0288 AC: 3217 AN: 111810 Hom.: 44 Cov.: 22 AF XY: 0.0276 AC XY: 938 AN XY: 33998

African (AFR) AF: 0.00565 AC: 174 AN: 30820

American (AMR) AF: 0.0125 AC: 132 AN: 10570

Ashkenazi Jewish (ASJ) AF: 0.00604 AC: 16 AN: 2649

East Asian (EAS) AF: 0.0132 AC: 47 AN: 3553

South Asian (SAS) AF: 0.0507 AC: 134 AN: 2643

European-Finnish (FIN) AF: 0.0499 AC: 301 AN: 6027

Middle Eastern (MID) AF: 0.00465 AC: 1 AN: 215

European-Non Finnish (NFE) AF: 0.0432 AC: 2294 AN: 53131

Other (OTH) AF: 0.0289 AC: 44 AN: 1520

Alfa AF: 0.0205 Hom.: 135

Bravo AF: 0.0248

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.010
DANN	Benign	0.88
PhyloP100		-1.6

Splicing

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

Other links and lift over

dbSNP: rs17340148; hg19: chrX-138648247;