rs1037212

Variant names:

• chrX-5103765-A-G
• rs1037212

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 0.97 (36303 hom., 32322 hem., cov: 24)
  • Failed GnomAD Quality Control
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.26
• Publications: 0 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.02).

Variant Effect in Transcripts

 

RefSeq Transcripts

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

Ensembl Transcripts

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

Frequencies

GnomAD3 genomes AF: 0.966 AC: 107418 AN: 111160 Hom.: 36304 Cov.: 24

Gnomad AFR AF: 0.974

Gnomad AMI AF: 0.978

Gnomad AMR AF: 0.977

Gnomad ASJ AF: 0.980

Gnomad EAS AF: 0.982

Gnomad SAS AF: 0.982

Gnomad FIN AF: 0.962

Gnomad MID AF: 0.983

Gnomad NFE AF: 0.958

Gnomad OTH AF: 0.963

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: 0.966 AC: 107479 AN: 111218 Hom.: 36303 Cov.: 24 AF XY: 0.968 AC XY: 32322 AN XY: 33394

African (AFR) AF: 0.975 AC: 29907 AN: 30689

American (AMR) AF: 0.977 AC: 10150 AN: 10391

Ashkenazi Jewish (ASJ) AF: 0.980 AC: 2588 AN: 2642

East Asian (EAS) AF: 0.982 AC: 3455 AN: 3517

South Asian (SAS) AF: 0.982 AC: 2573 AN: 2620

European-Finnish (FIN) AF: 0.962 AC: 5702 AN: 5930

Middle Eastern (MID) AF: 0.982 AC: 213 AN: 217

European-Non Finnish (NFE) AF: 0.958 AC: 50752 AN: 53003

Other (OTH) AF: 0.964 AC: 1468 AN: 1523

Alfa AF: 0.964 Hom.: 8787

Bravo AF: 0.969

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.68
DANN	Benign	0.27
PhyloP100		-1.3

Splicing

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

Other links and lift over

dbSNP: rs1037212; hg19: chrX-5021806;