X-76127599-G-A

Position:

• chrX-76127599-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 0.155 in 111,321 control chromosomes in the GnomAD database, including 1,059 homozygotes. There are 4,743 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 0.15 (1059 hom., 4743 hem., cov: 23)
• Consequence: intergenic_region
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.220

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.194 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
		n.76127599G>A		intergenic_region

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.155 AC: 17196 AN: 111268 Hom.: 1058 Cov.: 23 AF XY: 0.142 AC XY: 4743 AN XY: 33502

Gnomad AFR AF: 0.199

Gnomad AMI AF: 0.116

Gnomad AMR AF: 0.103

Gnomad ASJ AF: 0.142

Gnomad EAS AF: 0.00761

Gnomad SAS AF: 0.0890

Gnomad FIN AF: 0.130

Gnomad MID AF: 0.129

Gnomad NFE AF: 0.156

Gnomad OTH AF: 0.149

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

GnomAD4 genome AF: 0.155 AC: 17202 AN: 111321 Hom.: 1059 Cov.: 23 AF XY: 0.141 AC XY: 4743 AN XY: 33565

Gnomad4 AFR AF: 0.199

Gnomad4 AMR AF: 0.103

Gnomad4 ASJ AF: 0.142

Gnomad4 EAS AF: 0.00763

Gnomad4 SAS AF: 0.0877

Gnomad4 FIN AF: 0.130

Gnomad4 NFE AF: 0.157

Gnomad4 OTH AF: 0.154

Alfa AF: 0.155 Hom.: 8974

Bravo AF: 0.153

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	2.7
DANN	Benign	0.54

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs5937496; hg19: chrX-75347434;