rs2180237

Variant names:

• chrX-131988415-A-G
• rs2180237

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 0.94 (34731 hom., 31040 hem., cov: 23)
  • Failed GnomAD Quality Control
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0340
• Publications: 2 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).

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: 0.939 AC: 104289 AN: 111095 Hom.: 34729 Cov.: 23

Gnomad AFR AF: 0.990

Gnomad AMI AF: 0.978

Gnomad AMR AF: 0.878

Gnomad ASJ AF: 0.930

Gnomad EAS AF: 0.607

Gnomad SAS AF: 0.847

Gnomad FIN AF: 0.924

Gnomad MID AF: 0.941

Gnomad NFE AF: 0.950

Gnomad OTH AF: 0.921

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: 0.939 AC: 104347 AN: 111147 Hom.: 34731 Cov.: 23 AF XY: 0.932 AC XY: 31040 AN XY: 33313

African (AFR) AF: 0.989 AC: 30228 AN: 30549

American (AMR) AF: 0.878 AC: 9233 AN: 10515

Ashkenazi Jewish (ASJ) AF: 0.930 AC: 2453 AN: 2638

East Asian (EAS) AF: 0.606 AC: 2119 AN: 3494

South Asian (SAS) AF: 0.848 AC: 2214 AN: 2610

European-Finnish (FIN) AF: 0.924 AC: 5464 AN: 5915

Middle Eastern (MID) AF: 0.950 AC: 207 AN: 218

European-Non Finnish (NFE) AF: 0.950 AC: 50366 AN: 53007

Other (OTH) AF: 0.919 AC: 1399 AN: 1522

Alfa AF: 0.944 Hom.: 48865

Bravo AF: 0.934

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	1.9
DANN	Benign	0.44
PhyloP100		0.034

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs2180237;

hg19: chrX-131122443;