X-151829223-C-T

Variant names:

• chrX-151829223-C-T
• rs941400

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 0.484 in 110,764 control chromosomes in the GnomAD database, including 9,440 homozygotes. There are 15,690 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 0.48 (9440 hom., 15690 hem., cov: 23)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.597
• Publications: 2 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.58 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: 0.484 AC: 53567 AN: 110708 Hom.: 9444 Cov.: 23

Gnomad AFR AF: 0.541

Gnomad AMI AF: 0.681

Gnomad AMR AF: 0.592

Gnomad ASJ AF: 0.492

Gnomad EAS AF: 0.486

Gnomad SAS AF: 0.529

Gnomad FIN AF: 0.334

Gnomad MID AF: 0.583

Gnomad NFE AF: 0.440

Gnomad OTH AF: 0.531

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

GnomAD4 genome AF: 0.484 AC: 53605 AN: 110764 Hom.: 9440 Cov.: 23 AF XY: 0.475 AC XY: 15690 AN XY: 33050

African (AFR) AF: 0.542 AC: 16451 AN: 30377

American (AMR) AF: 0.592 AC: 6183 AN: 10441

Ashkenazi Jewish (ASJ) AF: 0.492 AC: 1295 AN: 2633

East Asian (EAS) AF: 0.486 AC: 1685 AN: 3470

South Asian (SAS) AF: 0.529 AC: 1387 AN: 2621

European-Finnish (FIN) AF: 0.334 AC: 1978 AN: 5925

Middle Eastern (MID) AF: 0.561 AC: 120 AN: 214

European-Non Finnish (NFE) AF: 0.440 AC: 23260 AN: 52913

Other (OTH) AF: 0.526 AC: 789 AN: 1499

Alfa AF: 0.463 Hom.: 13197

Bravo AF: 0.510

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	0.17
DANN	Benign	0.23
PhyloP100		-0.60

Splicing

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

Other links and lift over

dbSNP: rs941400; hg19: chrX-150997695;