rs41307258

Positions:

• chrX-80014614-T-A

Variant summary

Our verdict is Benign. Variant got -8 ACMG points: 1P and 9B. PP5 BP4 BA1

The variant allele was found at a frequency of 0.052 in 111,499 control chromosomes in the GnomAD database, including 301 homozygotes. There are 1,900 hemizygotes in GnomAD. In-silico tool predicts a benign outcome for this variant. Variant has been reported in Lovd as Likely pathogenic (no stars).

• Frequency:
  • Genomes: 𝑓 0.052 (301 hom., 1899 hem., cov: 23)
  • Exomes 𝑓: 0.14 (0 hom. 1 hem.)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.939

ACMG classification

Verdict is Benign. Variant got -8 ACMG points.

• PP5: Variant X-80014614-T-A is Pathogenic according to our data. Variant chrX-80014614-T-A is described in Lovd as [Likely_pathogenic].
• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.8). . Strength limited to SUPPORTING due to the PP5.
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.412 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: 0.0520 AC: 5793 AN: 111434 Hom.: 300 Cov.: 23 AF XY: 0.0565 AC XY: 1899 AN XY: 33640

Gnomad AFR AF: 0.0275

Gnomad AMI AF: 0.0570

Gnomad AMR AF: 0.0615

Gnomad ASJ AF: 0.0212

Gnomad EAS AF: 0.431

Gnomad SAS AF: 0.106

Gnomad FIN AF: 0.0961

Gnomad MID AF: 0.0252

Gnomad NFE AF: 0.0331

Gnomad OTH AF: 0.0662

GnomAD4 exome AF: 0.143 AC: 1 AN: 7 Hom.: 0 AF XY: 0.200 AC XY: 1 AN XY: 5

Gnomad4 AMR exome AF: 0.00

Gnomad4 NFE exome AF: 0.200

Gnomad4 OTH exome AF: 0.00

GnomAD4 genome AF: 0.0520 AC: 5800 AN: 111492 Hom.: 301 Cov.: 23 AF XY: 0.0563 AC XY: 1899 AN XY: 33708

Gnomad4 AFR AF: 0.0277

Gnomad4 AMR AF: 0.0617

Gnomad4 ASJ AF: 0.0212

Gnomad4 EAS AF: 0.430

Gnomad4 SAS AF: 0.106

Gnomad4 FIN AF: 0.0961

Gnomad4 NFE AF: 0.0331

Gnomad4 OTH AF: 0.0674

Alfa AF: 0.0404 Hom.: 208

Bravo AF: 0.0551

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.80
CADD	Benign	12
DANN	Benign	0.79

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs41307258; hg19: chrX-79270113;