chrX-51610701-G-A

Variant names:

• chrX-51610701-G-A
• rs1541242

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).

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: 0.856 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 v4.3

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;