X-114102638-C-T

Variant names:

• chrX-114102638-C-T
• rs5929434

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 0.432 in 110,522 control chromosomes in the GnomAD database, including 8,097 homozygotes. There are 14,390 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 0.43 (8097 hom., 14390 hem., cov: 22)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.791
• Publications: 1 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.7).
• 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: 0.432 AC: 47677 AN: 110467 Hom.: 8093 Cov.: 22

Gnomad AFR AF: 0.218

Gnomad AMI AF: 0.209

Gnomad AMR AF: 0.573

Gnomad ASJ AF: 0.469

Gnomad EAS AF: 0.846

Gnomad SAS AF: 0.620

Gnomad FIN AF: 0.557

Gnomad MID AF: 0.455

Gnomad NFE AF: 0.477

Gnomad OTH AF: 0.451

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

GnomAD4 genome AF: 0.432 AC: 47693 AN: 110522 Hom.: 8097 Cov.: 22 AF XY: 0.439 AC XY: 14390 AN XY: 32810

African (AFR) AF: 0.218 AC: 6663 AN: 30549

American (AMR) AF: 0.574 AC: 5922 AN: 10322

Ashkenazi Jewish (ASJ) AF: 0.469 AC: 1235 AN: 2635

East Asian (EAS) AF: 0.846 AC: 2917 AN: 3448

South Asian (SAS) AF: 0.620 AC: 1620 AN: 2611

European-Finnish (FIN) AF: 0.557 AC: 3239 AN: 5814

Middle Eastern (MID) AF: 0.455 AC: 96 AN: 211

European-Non Finnish (NFE) AF: 0.477 AC: 25166 AN: 52744

Other (OTH) AF: 0.458 AC: 694 AN: 1514

Alfa AF: 0.446 Hom.: 4782

Bravo AF: 0.430

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.70
CADD	Benign	6.3
DANN	Benign	0.74
PhyloP100		-0.79

Splicing

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

Other links and lift over

dbSNP: rs5929434; hg19: chrX-113345849;