rs1108444

chrX-114098062-C-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 0.436 in 110,135 control chromosomes in the GnomAD database, including 8,171 homozygotes. There are 14,434 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 0.44 (8171 hom., 14434 hem., cov: 22)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0730

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.82 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.436 AC: 48004 AN: 110086 Hom.: 8169 Cov.: 22 AF XY: 0.446 AC XY: 14419 AN XY: 32358

Gnomad AFR AF: 0.225

Gnomad AMI AF: 0.213

Gnomad AMR AF: 0.578

Gnomad ASJ AF: 0.487

Gnomad EAS AF: 0.846

Gnomad SAS AF: 0.631

Gnomad FIN AF: 0.568

Gnomad MID AF: 0.483

Gnomad NFE AF: 0.479

Gnomad OTH AF: 0.454

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

GnomAD4 genome AF: 0.436 AC: 48021 AN: 110135 Hom.: 8171 Cov.: 22 AF XY: 0.445 AC XY: 14434 AN XY: 32417

Gnomad4 AFR AF: 0.225

Gnomad4 AMR AF: 0.579

Gnomad4 ASJ AF: 0.487

Gnomad4 EAS AF: 0.846

Gnomad4 SAS AF: 0.633

Gnomad4 FIN AF: 0.568

Gnomad4 NFE AF: 0.479

Gnomad4 OTH AF: 0.462

Alfa AF: 0.477 Hom.: 23336

Bravo AF: 0.435

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
Cadd	Benign	3.4

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1108444; hg19: chrX-113341273;