rs1541242

Positions:

• chrX-51610701-G-A
• chrX-51610701-G-C
• chrX-51610701-G-T

Variant summary

Our verdict is Likely benign. Variant got -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 0.86 (28642 hom., 27723 hem., cov: 22)
  • Failed GnomAD Quality Control
• Consequence: intergenic_region
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.254

Genes affected

(HGNC:):

ACMG classification

Verdict is Likely_benign. Variant got -4 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
		n.51610701G>A		intergenic_region

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.856 AC: 94259 AN: 110179 Hom.: 28645 Cov.: 22 AF XY: 0.853 AC XY: 27665 AN XY: 32415

Gnomad AFR AF: 0.927

Gnomad AMI AF: 0.895

Gnomad AMR AF: 0.878

Gnomad ASJ AF: 0.866

Gnomad EAS AF: 0.960

Gnomad SAS AF: 0.854

Gnomad FIN AF: 0.777

Gnomad MID AF: 0.848

Gnomad NFE AF: 0.811

Gnomad OTH AF: 0.845

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: 0.856 AC: 94308 AN: 110231 Hom.: 28642 Cov.: 22 AF XY: 0.854 AC XY: 27723 AN XY: 32477

Gnomad4 AFR AF: 0.927

Gnomad4 AMR AF: 0.879

Gnomad4 ASJ AF: 0.866

Gnomad4 EAS AF: 0.960

Gnomad4 SAS AF: 0.853

Gnomad4 FIN AF: 0.777

Gnomad4 NFE AF: 0.811

Gnomad4 OTH AF: 0.847

Alfa AF: 0.823 Hom.: 30195

Bravo AF: 0.866

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	0.98
DANN	Benign	0.50

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1541242; hg19: chrX-51353553;