X-131988415-A-G

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).

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: 0.939 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 v4.3

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

Other links and lift over

dbSNP: rs2180237; hg19: chrX-131122443;