X-144934473-C-T

Variant names:

• chrX-144934473-C-T
• rs966187

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 0.267 in 108,059 control chromosomes in the GnomAD database, including 3,100 homozygotes. There are 7,998 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 0.27 (3100 hom., 7998 hem., cov: 21)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0750
• Publications: 0 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.01).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.377 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

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

Ensembl Transcripts

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

Frequencies

GnomAD3 genomes AF: 0.267 AC: 28820 AN: 108039 Hom.: 3097 Cov.: 21

Gnomad AFR AF: 0.383

Gnomad AMI AF: 0.0715

Gnomad AMR AF: 0.315

Gnomad ASJ AF: 0.279

Gnomad EAS AF: 0.345

Gnomad SAS AF: 0.306

Gnomad FIN AF: 0.207

Gnomad MID AF: 0.186

Gnomad NFE AF: 0.192

Gnomad OTH AF: 0.282

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

GnomAD4 genome AF: 0.267 AC: 28845 AN: 108059 Hom.: 3100 Cov.: 21 AF XY: 0.260 AC XY: 7998 AN XY: 30815

African (AFR) AF: 0.383 AC: 11412 AN: 29782

American (AMR) AF: 0.315 AC: 3165 AN: 10042

Ashkenazi Jewish (ASJ) AF: 0.279 AC: 727 AN: 2609

East Asian (EAS) AF: 0.344 AC: 1182 AN: 3435

South Asian (SAS) AF: 0.306 AC: 763 AN: 2496

European-Finnish (FIN) AF: 0.207 AC: 1108 AN: 5358

Middle Eastern (MID) AF: 0.191 AC: 39 AN: 204

European-Non Finnish (NFE) AF: 0.192 AC: 9977 AN: 51975

Other (OTH) AF: 0.287 AC: 423 AN: 1473

Alfa AF: 0.220 Hom.: 3452

Bravo AF: 0.287

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	2.1
DANN	Benign	0.27
PhyloP100		-0.075

Splicing

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

Other links and lift over

dbSNP: rs966187; hg19: chrX-144015993;