X-112864896-A-G

Position:

• chrX-112864896-A-G

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 0.37 in 110,314 control chromosomes in the GnomAD database, including 6,741 homozygotes. There are 11,655 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 0.37 (6741 hom., 11655 hem., cov: 22)
• Consequence: intergenic_region
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.221

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.594 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
		n.112864896A>G		intergenic_region

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.369 AC: 40737 AN: 110258 Hom.: 6736 Cov.: 22 AF XY: 0.357 AC XY: 11619 AN XY: 32536

Gnomad AFR AF: 0.601

Gnomad AMI AF: 0.196

Gnomad AMR AF: 0.478

Gnomad ASJ AF: 0.141

Gnomad EAS AF: 0.580

Gnomad SAS AF: 0.183

Gnomad FIN AF: 0.303

Gnomad MID AF: 0.258

Gnomad NFE AF: 0.233

Gnomad OTH AF: 0.361

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

GnomAD4 genome AF: 0.370 AC: 40773 AN: 110314 Hom.: 6741 Cov.: 22 AF XY: 0.358 AC XY: 11655 AN XY: 32600

Gnomad4 AFR AF: 0.601

Gnomad4 AMR AF: 0.478

Gnomad4 ASJ AF: 0.141

Gnomad4 EAS AF: 0.580

Gnomad4 SAS AF: 0.183

Gnomad4 FIN AF: 0.303

Gnomad4 NFE AF: 0.233

Gnomad4 OTH AF: 0.369

Alfa AF: 0.305 Hom.: 2180

Bravo AF: 0.403

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.38
DANN	Benign	0.42

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs648170; hg19: chrX-112108124;