X-55867932-T-C

Position:

• chrX-55867932-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 0.515 in 110,125 control chromosomes in the GnomAD database, including 12,923 homozygotes. There are 16,840 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 0.51 (12923 hom., 16840 hem., cov: 22)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.284

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.82).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.721 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: 0.515 AC: 56686 AN: 110069 Hom.: 12931 Cov.: 22 AF XY: 0.521 AC XY: 16837 AN XY: 32313

Gnomad AFR AF: 0.114

Gnomad AMI AF: 0.870

Gnomad AMR AF: 0.475

Gnomad ASJ AF: 0.499

Gnomad EAS AF: 0.745

Gnomad SAS AF: 0.640

Gnomad FIN AF: 0.783

Gnomad MID AF: 0.349

Gnomad NFE AF: 0.703

Gnomad OTH AF: 0.466

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

GnomAD4 genome AF: 0.515 AC: 56664 AN: 110125 Hom.: 12923 Cov.: 22 AF XY: 0.520 AC XY: 16840 AN XY: 32377

Gnomad4 AFR AF: 0.113

Gnomad4 AMR AF: 0.475

Gnomad4 ASJ AF: 0.499

Gnomad4 EAS AF: 0.745

Gnomad4 SAS AF: 0.641

Gnomad4 FIN AF: 0.783

Gnomad4 NFE AF: 0.703

Gnomad4 OTH AF: 0.460

Alfa AF: 0.619 Hom.: 15457

Bravo AF: 0.476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	3.9
DANN	Benign	0.80

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1536163; hg19: chrX-55894365;