chrX-55867932-T-C

Variant names:

• chrX-55867932-T-C
• rs1536163

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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	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;