rs454992

Variant names:

• chrX-149803773-T-C
• rs454992

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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	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;