X-116708191-G-A

Position:

• chrX-116708191-G-A

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The variant allele was found at a frequency of 0.122 in 110,608 control chromosomes in the GnomAD database, including 737 homozygotes. There are 3,865 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 0.12 (737 hom., 3865 hem., cov: 22)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: No conservation score assigned

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.177 is higher than 0.05.

Transcripts

RefSeq

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

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.122 AC: 13511 AN: 110550 Hom.: 739 Cov.: 22 AF XY: 0.118 AC XY: 3864 AN XY: 32776

Gnomad AFR AF: 0.0254

Gnomad AMI AF: 0.161

Gnomad AMR AF: 0.101

Gnomad ASJ AF: 0.0913

Gnomad EAS AF: 0.121

Gnomad SAS AF: 0.116

Gnomad FIN AF: 0.159

Gnomad MID AF: 0.0720

Gnomad NFE AF: 0.180

Gnomad OTH AF: 0.119

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

GnomAD4 genome AF: 0.122 AC: 13504 AN: 110608 Hom.: 737 Cov.: 22 AF XY: 0.118 AC XY: 3865 AN XY: 32844

Gnomad4 AFR AF: 0.0253

Gnomad4 AMR AF: 0.101

Gnomad4 ASJ AF: 0.0913

Gnomad4 EAS AF: 0.121

Gnomad4 SAS AF: 0.116

Gnomad4 FIN AF: 0.159

Gnomad4 NFE AF: 0.180

Gnomad4 OTH AF: 0.117

Alfa AF: 0.169 Hom.: 10606

Bravo AF: 0.115

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	2.8
DANN	Benign	0.71

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs5911500; hg19: chrX-115842159;