rs989345

Variant names:

• chrX-67081192-G-A
• rs989345

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 0.66 (20451 hom., 21306 hem., cov: 22)
  • Failed GnomAD Quality Control
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.402
• Publications: 4 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: 0.658 AC: 72065 AN: 109582 Hom.: 20459 Cov.: 22

Gnomad AFR AF: 0.155

Gnomad AMI AF: 0.884

Gnomad AMR AF: 0.832

Gnomad ASJ AF: 0.918

Gnomad EAS AF: 0.998

Gnomad SAS AF: 0.921

Gnomad FIN AF: 0.830

Gnomad MID AF: 0.762

Gnomad NFE AF: 0.843

Gnomad OTH AF: 0.705

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: 0.657 AC: 72050 AN: 109624 Hom.: 20451 Cov.: 22 AF XY: 0.668 AC XY: 21306 AN XY: 31908

African (AFR) AF: 0.155 AC: 4697 AN: 30386

American (AMR) AF: 0.832 AC: 8446 AN: 10146

Ashkenazi Jewish (ASJ) AF: 0.918 AC: 2417 AN: 2632

East Asian (EAS) AF: 0.998 AC: 3450 AN: 3456

South Asian (SAS) AF: 0.920 AC: 2294 AN: 2493

European-Finnish (FIN) AF: 0.830 AC: 4653 AN: 5607

Middle Eastern (MID) AF: 0.758 AC: 160 AN: 211

European-Non Finnish (NFE) AF: 0.843 AC: 44289 AN: 52536

Other (OTH) AF: 0.706 AC: 1044 AN: 1478

Alfa AF: 0.786 Hom.: 115509

Bravo AF: 0.641

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.45
DANN	Benign	0.29
PhyloP100		-0.40

Splicing

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

Other links and lift over

dbSNP: rs989345; hg19: chrX-66301034;