rs56204867

Positions:

• chrX-129656490-A-G

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 0.107 in 108,334 control chromosomes in the GnomAD database, including 1,072 homozygotes. There are 2,982 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 0.11 (1072 hom., 2982 hem., cov: 21)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.241

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 = 0.352 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.107 AC: 11610 AN: 108308 Hom.: 1072 Cov.: 21 AF XY: 0.0962 AC XY: 2975 AN XY: 30938

Gnomad AFR AF: 0.274

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0655

Gnomad ASJ AF: 0.00420

Gnomad EAS AF: 0.368

Gnomad SAS AF: 0.109

Gnomad FIN AF: 0.0101

Gnomad MID AF: 0.0468

Gnomad NFE AF: 0.0215

Gnomad OTH AF: 0.0962

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

GnomAD4 genome AF: 0.107 AC: 11617 AN: 108334 Hom.: 1072 Cov.: 21 AF XY: 0.0963 AC XY: 2982 AN XY: 30976

Gnomad4 AFR AF: 0.274

Gnomad4 AMR AF: 0.0659

Gnomad4 ASJ AF: 0.00420

Gnomad4 EAS AF: 0.369

Gnomad4 SAS AF: 0.109

Gnomad4 FIN AF: 0.0101

Gnomad4 NFE AF: 0.0215

Gnomad4 OTH AF: 0.0951

Alfa AF: 0.0662 Hom.: 354

Bravo AF: 0.126

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	1.7
DANN	Benign	0.83

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs56204867; hg19: chrX-128790467;