rs1541242

Variant names:

• chrX-51610701-G-A
• rs1541242

Your query was ambiguous. Multiple possible variants found:

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

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 0.86 (28642 hom., 27723 hem., cov: 22)
  • Failed GnomAD Quality Control
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.254
• Publications: 3 publications found

ACMG classification

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

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

Variant Effect in Transcripts

 

RefSeq Transcripts

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

Ensembl Transcripts

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

Frequencies

GnomAD3 genomes AF: 0.856 AC: 94259 AN: 110179 Hom.: 28645 Cov.: 22

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

African (AFR) AF: 0.927 AC: 28154 AN: 30375

American (AMR) AF: 0.879 AC: 9064 AN: 10317

Ashkenazi Jewish (ASJ) AF: 0.866 AC: 2287 AN: 2640

East Asian (EAS) AF: 0.960 AC: 3363 AN: 3504

South Asian (SAS) AF: 0.853 AC: 2169 AN: 2543

European-Finnish (FIN) AF: 0.777 AC: 4473 AN: 5757

Middle Eastern (MID) AF: 0.837 AC: 180 AN: 215

European-Non Finnish (NFE) AF: 0.811 AC: 42753 AN: 52717

Other (OTH) AF: 0.847 AC: 1260 AN: 1487

Alfa AF: 0.827 Hom.: 53388

Bravo AF: 0.866

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	0.98
DANN	Benign	0.50
PhyloP100		0.25

Splicing

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

Other links and lift over

dbSNP: rs1541242; hg19: chrX-51353553;