X-112864517-G-C

Position:

• chrX-112864517-G-C

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 0.353 in 110,786 control chromosomes in the GnomAD database, including 5,946 homozygotes. There are 11,380 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 0.35 (5946 hom., 11380 hem., cov: 23)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.166

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 (EAS) allele frequency at 95% confidence interval = 0.563 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: 0.353 AC: 39043 AN: 110734 Hom.: 5942 Cov.: 23 AF XY: 0.344 AC XY: 11353 AN XY: 32988

Gnomad AFR AF: 0.542

Gnomad AMI AF: 0.202

Gnomad AMR AF: 0.472

Gnomad ASJ AF: 0.139

Gnomad EAS AF: 0.585

Gnomad SAS AF: 0.184

Gnomad FIN AF: 0.306

Gnomad MID AF: 0.241

Gnomad NFE AF: 0.233

Gnomad OTH AF: 0.336

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

GnomAD4 genome AF: 0.353 AC: 39069 AN: 110786 Hom.: 5946 Cov.: 23 AF XY: 0.344 AC XY: 11380 AN XY: 33050

Gnomad4 AFR AF: 0.542

Gnomad4 AMR AF: 0.472

Gnomad4 ASJ AF: 0.139

Gnomad4 EAS AF: 0.584

Gnomad4 SAS AF: 0.183

Gnomad4 FIN AF: 0.306

Gnomad4 NFE AF: 0.233

Gnomad4 OTH AF: 0.345

Alfa AF: 0.150 Hom.: 720

Bravo AF: 0.383

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	1.7
DANN	Benign	0.48

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs547425; hg19: chrX-112107745;