X-122833506-C-T

Variant names:

• chrX-122833506-C-T
• rs4559365

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 0.386 in 110,221 control chromosomes in the GnomAD database, including 6,257 homozygotes. There are 12,240 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 0.39 (6257 hom., 12240 hem., cov: 22)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.192
• Publications: 2 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.522 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: 0.386 AC: 42482 AN: 110167 Hom.: 6257 Cov.: 22

Gnomad AFR AF: 0.528

Gnomad AMI AF: 0.240

Gnomad AMR AF: 0.312

Gnomad ASJ AF: 0.321

Gnomad EAS AF: 0.203

Gnomad SAS AF: 0.473

Gnomad FIN AF: 0.339

Gnomad MID AF: 0.333

Gnomad NFE AF: 0.337

Gnomad OTH AF: 0.348

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

GnomAD4 genome AF: 0.386 AC: 42500 AN: 110221 Hom.: 6257 Cov.: 22 AF XY: 0.376 AC XY: 12240 AN XY: 32531

African (AFR) AF: 0.528 AC: 16016 AN: 30309

American (AMR) AF: 0.312 AC: 3228 AN: 10337

Ashkenazi Jewish (ASJ) AF: 0.321 AC: 844 AN: 2630

East Asian (EAS) AF: 0.203 AC: 710 AN: 3491

South Asian (SAS) AF: 0.469 AC: 1230 AN: 2623

European-Finnish (FIN) AF: 0.339 AC: 1954 AN: 5764

Middle Eastern (MID) AF: 0.324 AC: 69 AN: 213

European-Non Finnish (NFE) AF: 0.337 AC: 17768 AN: 52672

Other (OTH) AF: 0.345 AC: 518 AN: 1503

Alfa AF: 0.363 Hom.: 22601

Bravo AF: 0.391

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.84
DANN	Benign	0.48
PhyloP100		-0.19

Splicing

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

Other links and lift over

dbSNP: rs4559365; hg19: chrX-121967359; COSMIC: COSV107184838;