chrX-854110-G-C

Variant names:

• chrX-854110-G-C
• rs5988281

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 0.299 in 151,246 control chromosomes in the GnomAD database, including 7,551 homozygotes. There are 22,162 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 0.30 (7551 hom., 22162 hem., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.00

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.441 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: 0.299 AC: 45160 AN: 151124 Hom.: 7537 Cov.: 31 AF XY: 0.300 AC XY: 22103 AN XY: 73750

Gnomad AFR AF: 0.446

Gnomad AMI AF: 0.158

Gnomad AMR AF: 0.292

Gnomad ASJ AF: 0.205

Gnomad EAS AF: 0.453

Gnomad SAS AF: 0.387

Gnomad FIN AF: 0.223

Gnomad MID AF: 0.302

Gnomad NFE AF: 0.212

Gnomad OTH AF: 0.278

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

GnomAD4 genome AF: 0.299 AC: 45204 AN: 151246 Hom.: 7551 Cov.: 31 AF XY: 0.300 AC XY: 22162 AN XY: 73880

Gnomad4 AFR AF: 0.446

Gnomad4 AMR AF: 0.292

Gnomad4 ASJ AF: 0.205

Gnomad4 EAS AF: 0.453

Gnomad4 SAS AF: 0.385

Gnomad4 FIN AF: 0.223

Gnomad4 NFE AF: 0.212

Gnomad4 OTH AF: 0.276

Bravo AF: 0.307

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	0.69
DANN	Benign	0.29

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs5988281; hg19: chrX-814845;