chrX-42989135-T-C

Variant names:

• chrX-42989135-T-C
• rs1983167

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 0.71 (19867 hom., 22720 hem., cov: 22)
  • Failed GnomAD Quality Control
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.436
• Publications: 1 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).

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: 0.710 AC: 77839 AN: 109631 Hom.: 19858 Cov.: 22

Gnomad AFR AF: 0.788

Gnomad AMI AF: 0.601

Gnomad AMR AF: 0.723

Gnomad ASJ AF: 0.617

Gnomad EAS AF: 0.913

Gnomad SAS AF: 0.817

Gnomad FIN AF: 0.730

Gnomad MID AF: 0.604

Gnomad NFE AF: 0.649

Gnomad OTH AF: 0.690

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: 0.710 AC: 77901 AN: 109686 Hom.: 19867 Cov.: 22 AF XY: 0.711 AC XY: 22720 AN XY: 31940

African (AFR) AF: 0.788 AC: 23768 AN: 30160

American (AMR) AF: 0.723 AC: 7406 AN: 10240

Ashkenazi Jewish (ASJ) AF: 0.617 AC: 1619 AN: 2622

East Asian (EAS) AF: 0.913 AC: 3163 AN: 3463

South Asian (SAS) AF: 0.820 AC: 2074 AN: 2528

European-Finnish (FIN) AF: 0.730 AC: 4164 AN: 5701

Middle Eastern (MID) AF: 0.586 AC: 126 AN: 215

European-Non Finnish (NFE) AF: 0.649 AC: 34143 AN: 52593

Other (OTH) AF: 0.693 AC: 1034 AN: 1492

Alfa AF: 0.693 Hom.: 7503

Bravo AF: 0.718

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	1.9
DANN	Benign	0.65
PhyloP100		-0.44

Splicing

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

Other links and lift over

dbSNP: rs1983167; hg19: chrX-42848384;