X-12865772-C-T

Variant names:

• chrX-12865772-C-T
• rs5935436

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 0.154 in 111,093 control chromosomes in the GnomAD database, including 1,268 homozygotes. There are 4,737 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 0.15 (1268 hom., 4737 hem., cov: 22)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.215
• Publications: 11 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.272 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: 0.154 AC: 17070 AN: 111042 Hom.: 1267 Cov.: 22

Gnomad AFR AF: 0.276

Gnomad AMI AF: 0.221

Gnomad AMR AF: 0.124

Gnomad ASJ AF: 0.136

Gnomad EAS AF: 0.0391

Gnomad SAS AF: 0.157

Gnomad FIN AF: 0.0686

Gnomad MID AF: 0.238

Gnomad NFE AF: 0.106

Gnomad OTH AF: 0.171

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

GnomAD4 genome AF: 0.154 AC: 17086 AN: 111093 Hom.: 1268 Cov.: 22 AF XY: 0.142 AC XY: 4737 AN XY: 33333

African (AFR) AF: 0.277 AC: 8412 AN: 30400

American (AMR) AF: 0.124 AC: 1296 AN: 10471

Ashkenazi Jewish (ASJ) AF: 0.136 AC: 359 AN: 2635

East Asian (EAS) AF: 0.0389 AC: 138 AN: 3546

South Asian (SAS) AF: 0.156 AC: 415 AN: 2654

European-Finnish (FIN) AF: 0.0686 AC: 410 AN: 5974

Middle Eastern (MID) AF: 0.248 AC: 54 AN: 218

European-Non Finnish (NFE) AF: 0.106 AC: 5600 AN: 53023

Other (OTH) AF: 0.169 AC: 254 AN: 1501

Alfa AF: 0.118 Hom.: 6115

Bravo AF: 0.166

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	6.0
DANN	Benign	0.69
PhyloP100		-0.21

Splicing

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

Other links and lift over

dbSNP: rs5935436; hg19: chrX-12883891;