X-920377-G-C

Position:

• chrX-920377-G-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 0.635 in 151,928 control chromosomes in the GnomAD database, including 31,541 homozygotes. There are 47,387 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 0.63 (31541 hom., 47387 hem., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.754

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.7).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.766 is higher than 0.05.

Transcripts

RefSeq

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

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.635 AC: 96356 AN: 151810 Hom.: 31508 Cov.: 32 AF XY: 0.638 AC XY: 47290 AN XY: 74074

Gnomad AFR AF: 0.773

Gnomad AMI AF: 0.563

Gnomad AMR AF: 0.634

Gnomad ASJ AF: 0.714

Gnomad EAS AF: 0.779

Gnomad SAS AF: 0.781

Gnomad FIN AF: 0.556

Gnomad MID AF: 0.712

Gnomad NFE AF: 0.538

Gnomad OTH AF: 0.639

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

GnomAD4 genome AF: 0.635 AC: 96434 AN: 151928 Hom.: 31541 Cov.: 32 AF XY: 0.639 AC XY: 47387 AN XY: 74202

Gnomad4 AFR AF: 0.773

Gnomad4 AMR AF: 0.634

Gnomad4 ASJ AF: 0.714

Gnomad4 EAS AF: 0.778

Gnomad4 SAS AF: 0.780

Gnomad4 FIN AF: 0.556

Gnomad4 NFE AF: 0.538

Gnomad4 OTH AF: 0.630

Bravo AF: 0.646

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.70
CADD	Benign	0.19
DANN	Benign	0.26

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs5988494; hg19: chrX-881112;