rs12557549

Variant names:

• chrX-67523723-C-T
• rs12557549

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BS1 BS2

The variant allele was found at a frequency of 0.0121 in 110,785 control chromosomes in the GnomAD database, including 8 homozygotes. There are 375 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 0.012 (8 hom., 375 hem., cov: 22)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.00
• 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).
• BS1: Variant frequency is greater than expected in population amr. GnomAd4 allele frequency = 0.0121 (1345/110785) while in subpopulation AMR AF = 0.02 (208/10388). AF 95% confidence interval is 0.0178. There are 8 homozygotes in GnomAd4. There are 375 alleles in the male GnomAd4 subpopulation. Median coverage is 22. This position passed quality control check.
• BS2: High Homozygotes in GnomAd4 at 8 gene

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: 0.0122 AC: 1348 AN: 110733 Hom.: 8 Cov.: 22

Gnomad AFR AF: 0.00227

Gnomad AMI AF: 0.00730

Gnomad AMR AF: 0.0201

Gnomad ASJ AF: 0.0110

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.00348

Gnomad FIN AF: 0.00202

Gnomad MID AF: 0.0417

Gnomad NFE AF: 0.0184

Gnomad OTH AF: 0.0208

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

GnomAD4 genome AF: 0.0121 AC: 1345 AN: 110785 Hom.: 8 Cov.: 22 AF XY: 0.0113 AC XY: 375 AN XY: 33097

African (AFR) AF: 0.00226 AC: 69 AN: 30474

American (AMR) AF: 0.0200 AC: 208 AN: 10388

Ashkenazi Jewish (ASJ) AF: 0.0110 AC: 29 AN: 2646

East Asian (EAS) AF: 0.00 AC: 0 AN: 3460

South Asian (SAS) AF: 0.00350 AC: 9 AN: 2574

European-Finnish (FIN) AF: 0.00202 AC: 12 AN: 5949

Middle Eastern (MID) AF: 0.0411 AC: 9 AN: 219

European-Non Finnish (NFE) AF: 0.0184 AC: 974 AN: 52883

Other (OTH) AF: 0.0199 AC: 30 AN: 1507

Alfa AF: 0.0150 Hom.: 97

Bravo AF: 0.0142

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.12
DANN	Benign	0.50
PhyloP100		-1.0

Splicing

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

Other links and lift over

dbSNP: rs12557549; hg19: chrX-66743565;