rs1108444

Variant names:

• chrX-114098062-C-A
• rs1108444

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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	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;