rs454992

Positions:

• chrX-149803773-T-C

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The variant allele was found at a frequency of 0.212 in 111,249 control chromosomes in the GnomAD database, including 1,942 homozygotes. There are 6,761 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 0.21 (1942 hom., 6761 hem., cov: 23)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.337

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.308 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.212 AC: 23579 AN: 111194 Hom.: 1941 Cov.: 23 AF XY: 0.201 AC XY: 6733 AN XY: 33448

Gnomad AFR AF: 0.313

Gnomad AMI AF: 0.119

Gnomad AMR AF: 0.133

Gnomad ASJ AF: 0.211

Gnomad EAS AF: 0.0711

Gnomad SAS AF: 0.163

Gnomad FIN AF: 0.191

Gnomad MID AF: 0.214

Gnomad NFE AF: 0.187

Gnomad OTH AF: 0.176

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

GnomAD4 genome AF: 0.212 AC: 23611 AN: 111249 Hom.: 1942 Cov.: 23 AF XY: 0.202 AC XY: 6761 AN XY: 33513

Gnomad4 AFR AF: 0.314

Gnomad4 AMR AF: 0.133

Gnomad4 ASJ AF: 0.211

Gnomad4 EAS AF: 0.0711

Gnomad4 SAS AF: 0.164

Gnomad4 FIN AF: 0.191

Gnomad4 NFE AF: 0.187

Gnomad4 OTH AF: 0.175

Alfa AF: 0.193 Hom.: 1313

Bravo AF: 0.210

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	2.2
DANN	Benign	0.72

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs454992; hg19: chrX-148885435;