X-134459991-T-G

Position:

• chrX-134459991-T-G

Variant summary

Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_Strong BP6_Moderate BA1

The variant allele was found at a frequency of 0.501 in 108,661 control chromosomes in the GnomAD database, including 11,491 homozygotes. There are 15,279 hemizygotes in GnomAD. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

• Frequency: Genomes: 𝑓 0.50 (11491 hom., 15279 hem., cov: 21)
• Consequence: intergenic_region
• Clinical Significance: Benign criteria provided, single submitter B:1
• Conservation: PhyloP100: -4.15

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -14 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.8).
• BP6: Variant X-134459991-T-G is Benign according to our data. Variant chrX-134459991-T-G is described in ClinVar as [Benign]. Clinvar id is 1273471.Status of the report is criteria_provided_single_submitter, 1 stars.
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.778 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
		n.134459991T>G		intergenic_region

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.501 AC: 54412 AN: 108611 Hom.: 11491 Cov.: 21 AF XY: 0.490 AC XY: 15227 AN XY: 31045

Gnomad AFR AF: 0.786

Gnomad AMI AF: 0.280

Gnomad AMR AF: 0.553

Gnomad ASJ AF: 0.332

Gnomad EAS AF: 0.653

Gnomad SAS AF: 0.425

Gnomad FIN AF: 0.364

Gnomad MID AF: 0.316

Gnomad NFE AF: 0.349

Gnomad OTH AF: 0.497

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

GnomAD4 genome AF: 0.501 AC: 54463 AN: 108661 Hom.: 11491 Cov.: 21 AF XY: 0.491 AC XY: 15279 AN XY: 31105

Gnomad4 AFR AF: 0.786

Gnomad4 AMR AF: 0.554

Gnomad4 ASJ AF: 0.332

Gnomad4 EAS AF: 0.653

Gnomad4 SAS AF: 0.426

Gnomad4 FIN AF: 0.364

Gnomad4 NFE AF: 0.349

Gnomad4 OTH AF: 0.495

Alfa AF: 0.359 Hom.: 7196

Bravo AF: 0.536

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

Submissions by phenotype

not provided Benign:1

Benign, criteria provided, single submitter

clinical testing

GeneDx

Feb 03, 2020

- -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.80
CADD	Benign	0.48
DANN	Benign	0.24

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6634990; hg19: chrX-133594021;