rs1108444

Variant names:

• chrX-114098062-C-A
• rs1108444

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 3 publications found

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Frequencies

GnomAD3 genomes AF: 0.436 AC: 48004 AN: 110086 Hom.: 8169 Cov.: 22

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

African (AFR) AF: 0.225 AC: 6830 AN: 30423

American (AMR) AF: 0.579 AC: 5942 AN: 10263

Ashkenazi Jewish (ASJ) AF: 0.487 AC: 1283 AN: 2633

East Asian (EAS) AF: 0.846 AC: 2914 AN: 3445

South Asian (SAS) AF: 0.633 AC: 1642 AN: 2594

European-Finnish (FIN) AF: 0.568 AC: 3261 AN: 5737

Middle Eastern (MID) AF: 0.481 AC: 103 AN: 214

European-Non Finnish (NFE) AF: 0.479 AC: 25211 AN: 52652

Other (OTH) AF: 0.462 AC: 691 AN: 1497

Alfa AF: 0.466 Hom.: 35475

Bravo AF: 0.435

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	3.4
PhyloP100		0.073

Splicing

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

Other links and lift over

dbSNP: rs1108444; hg19: chrX-113341273;