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).

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: 0.966 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 v4.3

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;