rs1558022

Variant names:

• chrX-117374356-C-T
• rs1558022

Variant summary

Our verdict is Likely benign. The variant received -4 ACMG points: 0P and 4B. BP4_Strong

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 0.65 (17200 hom., 22014 hem., cov: 23)
  • Failed GnomAD Quality Control
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.00100
• Publications: 4 publications found

ACMG classification

Our verdict: Likely_benign. The variant received -4 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).

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: 0.652 AC: 72374 AN: 111060 Hom.: 17192 Cov.: 23

Gnomad AFR AF: 0.814

Gnomad AMI AF: 0.437

Gnomad AMR AF: 0.742

Gnomad ASJ AF: 0.565

Gnomad EAS AF: 0.998

Gnomad SAS AF: 0.858

Gnomad FIN AF: 0.575

Gnomad MID AF: 0.513

Gnomad NFE AF: 0.523

Gnomad OTH AF: 0.632

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

GnomAD4 genome Data not reliable, filtered out with message: InbreedingCoeff AF: 0.652 AC: 72430 AN: 111110 Hom.: 17200 Cov.: 23 AF XY: 0.660 AC XY: 22014 AN XY: 33362

African (AFR) AF: 0.814 AC: 24936 AN: 30625

American (AMR) AF: 0.742 AC: 7778 AN: 10476

Ashkenazi Jewish (ASJ) AF: 0.565 AC: 1490 AN: 2636

East Asian (EAS) AF: 0.998 AC: 3514 AN: 3521

South Asian (SAS) AF: 0.856 AC: 2258 AN: 2637

European-Finnish (FIN) AF: 0.575 AC: 3414 AN: 5936

Middle Eastern (MID) AF: 0.512 AC: 109 AN: 213

European-Non Finnish (NFE) AF: 0.523 AC: 27674 AN: 52884

Other (OTH) AF: 0.638 AC: 963 AN: 1509

Alfa AF: 0.598 Hom.: 22805

Bravo AF: 0.673

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	1.4
DANN	Benign	0.26
PhyloP100		0.0010

Splicing

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

Other links and lift over

dbSNP: rs1558022; hg19: chrX-116508319;