X-890391-C-G

Variant names:

• chrX-890391-C-G
• rs5988459

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 0.4 in 152,020 control chromosomes in the GnomAD database, including 15,970 homozygotes. There are 30,275 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 0.40 (15970 hom., 30275 hem., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.60

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.746 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: 0.400 AC: 60755 AN: 151902 Hom.: 15934 Cov.: 32 AF XY: 0.407 AC XY: 30172 AN XY: 74142

Gnomad AFR AF: 0.703

Gnomad AMI AF: 0.421

Gnomad AMR AF: 0.385

Gnomad ASJ AF: 0.288

Gnomad EAS AF: 0.767

Gnomad SAS AF: 0.510

Gnomad FIN AF: 0.288

Gnomad MID AF: 0.344

Gnomad NFE AF: 0.207

Gnomad OTH AF: 0.364

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

GnomAD4 genome AF: 0.400 AC: 60841 AN: 152020 Hom.: 15970 Cov.: 32 AF XY: 0.408 AC XY: 30275 AN XY: 74270

Gnomad4 AFR AF: 0.704

Gnomad4 AMR AF: 0.385

Gnomad4 ASJ AF: 0.288

Gnomad4 EAS AF: 0.766

Gnomad4 SAS AF: 0.509

Gnomad4 FIN AF: 0.288

Gnomad4 NFE AF: 0.207

Gnomad4 OTH AF: 0.362

Bravo AF: 0.424

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	0.95
DANN	Benign	0.46

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs5988459; hg19: chrX-851126;