rs477233

Positions:

• chrX-23687058-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 0.426 in 109,640 control chromosomes in the GnomAD database, including 7,274 homozygotes. There are 13,299 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 0.43 (7274 hom., 13299 hem., cov: 22)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.231

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.481 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: 0.426 AC: 46726 AN: 109586 Hom.: 7280 Cov.: 22 AF XY: 0.416 AC XY: 13272 AN XY: 31920

Gnomad AFR AF: 0.422

Gnomad AMI AF: 0.413

Gnomad AMR AF: 0.477

Gnomad ASJ AF: 0.516

Gnomad EAS AF: 0.502

Gnomad SAS AF: 0.337

Gnomad FIN AF: 0.411

Gnomad MID AF: 0.509

Gnomad NFE AF: 0.415

Gnomad OTH AF: 0.443

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

GnomAD4 genome AF: 0.426 AC: 46742 AN: 109640 Hom.: 7274 Cov.: 22 AF XY: 0.416 AC XY: 13299 AN XY: 31984

Gnomad4 AFR AF: 0.421

Gnomad4 AMR AF: 0.477

Gnomad4 ASJ AF: 0.516

Gnomad4 EAS AF: 0.501

Gnomad4 SAS AF: 0.336

Gnomad4 FIN AF: 0.411

Gnomad4 NFE AF: 0.415

Gnomad4 OTH AF: 0.448

Alfa AF: 0.427 Hom.: 41483

Bravo AF: 0.440

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	8.5
DANN	Benign	0.89

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs477233; hg19: chrX-23705175;