chrX-139566088-C-T

Position:

• chrX-139566088-C-T

Variant summary

Our verdict is Benign. Variant got -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: intergenic_region
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.58

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -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 male gnomad4 subpopulation. Median coverage is 22. This position pass quality control queck.
• BS2: High Homozygotes in GnomAd4 at 44 gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
		n.139566088C>T		intergenic_region

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.0288 AC: 3219 AN: 111757 Hom.: 44 Cov.: 22 AF XY: 0.0276 AC XY: 938 AN XY: 33935

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

Gnomad4 AFR AF: 0.00565

Gnomad4 AMR AF: 0.0125

Gnomad4 ASJ AF: 0.00604

Gnomad4 EAS AF: 0.0132

Gnomad4 SAS AF: 0.0507

Gnomad4 FIN AF: 0.0499

Gnomad4 NFE AF: 0.0432

Gnomad4 OTH AF: 0.0289

Alfa AF: 0.0205 Hom.: 135

Bravo AF: 0.0248

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs17340148; hg19: chrX-138648247;