rs56204867

Variant names:

• chrX-129656490-A-G
• rs56204867

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 21 publications found

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

 

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Frequencies

GnomAD3 genomes AF: 0.107 AC: 11610 AN: 108308 Hom.: 1072 Cov.: 21

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

African (AFR) AF: 0.274 AC: 8082 AN: 29509

American (AMR) AF: 0.0659 AC: 674 AN: 10225

Ashkenazi Jewish (ASJ) AF: 0.00420 AC: 11 AN: 2622

East Asian (EAS) AF: 0.369 AC: 1254 AN: 3402

South Asian (SAS) AF: 0.109 AC: 266 AN: 2446

European-Finnish (FIN) AF: 0.0101 AC: 54 AN: 5372

Middle Eastern (MID) AF: 0.0421 AC: 9 AN: 214

European-Non Finnish (NFE) AF: 0.0215 AC: 1127 AN: 52389

Other (OTH) AF: 0.0951 AC: 140 AN: 1472

Alfa AF: 0.0662 Hom.: 354

Bravo AF: 0.126

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	1.7
DANN	Benign	0.83
PhyloP100		0.24

Splicing

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

Other links and lift over

dbSNP: rs56204867; hg19: chrX-128790467;