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).

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: 0.979 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 v4.3

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;