rs12557549

Positions:

• chrX-67523723-C-T

Variant summary

Our verdict is Benign. Variant got -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: intergenic_region
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.00

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -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 male gnomad4 subpopulation. Median coverage is 22. This position pass quality control queck.
• BS2: High Homozygotes in GnomAd4 at 8 gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
		n.67523723C>T		intergenic_region

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.0122 AC: 1348 AN: 110733 Hom.: 8 Cov.: 22 AF XY: 0.0114 AC XY: 375 AN XY: 33035

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

Gnomad4 AFR AF: 0.00226

Gnomad4 AMR AF: 0.0200

Gnomad4 ASJ AF: 0.0110

Gnomad4 EAS AF: 0.00

Gnomad4 SAS AF: 0.00350

Gnomad4 FIN AF: 0.00202

Gnomad4 NFE AF: 0.0184

Gnomad4 OTH AF: 0.0199

Alfa AF: 0.0150 Hom.: 97

Bravo AF: 0.0142

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs12557549; hg19: chrX-66743565;