X-43883413-A-G

Variant names:

• chrX-43883413-A-G
• rs1181252

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 0.98 (37325 hom., 31789 hem., cov: 23)
  • Failed GnomAD Quality Control
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.470
• 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=-0.97).

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: 0.979 AC: 107948 AN: 110273 Hom.: 37328 Cov.: 23

Gnomad AFR AF: 0.995

Gnomad AMI AF: 0.994

Gnomad AMR AF: 0.985

Gnomad ASJ AF: 0.995

Gnomad EAS AF: 1.00

Gnomad SAS AF: 0.977

Gnomad FIN AF: 0.955

Gnomad MID AF: 0.996

Gnomad NFE AF: 0.968

Gnomad OTH AF: 0.981

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: 0.979 AC: 108004 AN: 110327 Hom.: 37325 Cov.: 23 AF XY: 0.978 AC XY: 31789 AN XY: 32497

African (AFR) AF: 0.995 AC: 30176 AN: 30317

American (AMR) AF: 0.985 AC: 10205 AN: 10361

Ashkenazi Jewish (ASJ) AF: 0.995 AC: 2622 AN: 2635

East Asian (EAS) AF: 1.00 AC: 3504 AN: 3504

South Asian (SAS) AF: 0.977 AC: 2436 AN: 2494

European-Finnish (FIN) AF: 0.955 AC: 5516 AN: 5774

Middle Eastern (MID) AF: 0.995 AC: 216 AN: 217

European-Non Finnish (NFE) AF: 0.969 AC: 51172 AN: 52836

Other (OTH) AF: 0.981 AC: 1481 AN: 1509

Alfa AF: 0.970 Hom.: 17200

Bravo AF: 0.981

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	0.16
DANN	Benign	0.50
PhyloP100		-0.47

Splicing

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

Other links and lift over

dbSNP: rs1181252; hg19: chrX-43742659;