rs1037212

chrX-5103765-A-G

Variant summary

Our verdict is Benign. Variant got -8 ACMG points: 0P and 8B. BP4_Strong BS2

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

ACMG classification

Verdict is Benign. Variant got -8 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.02).
• BS2: High Homozygotes in GnomAd at 36304 gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.966 AC: 107418 AN: 111160 Hom.: 36304 Cov.: 24 AF XY: 0.968 AC XY: 32255 AN XY: 33326

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

Gnomad4 AFR AF: 0.975

Gnomad4 AMR AF: 0.977

Gnomad4 ASJ AF: 0.980

Gnomad4 EAS AF: 0.982

Gnomad4 SAS AF: 0.982

Gnomad4 FIN AF: 0.962

Gnomad4 NFE AF: 0.958

Gnomad4 OTH AF: 0.964

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1037212; hg19: chrX-5021806;