rs1930674

Variant names:

• chrX-145010077-G-C
• rs1930674

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 0.56 (12332 hom., 18052 hem., cov: 23)
  • Failed GnomAD Quality Control
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.634
• 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=-1.02).

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: 0.561 AC: 61713 AN: 110055 Hom.: 12328 Cov.: 23

Gnomad AFR AF: 0.576

Gnomad AMI AF: 0.443

Gnomad AMR AF: 0.540

Gnomad ASJ AF: 0.593

Gnomad EAS AF: 0.554

Gnomad SAS AF: 0.525

Gnomad FIN AF: 0.569

Gnomad MID AF: 0.457

Gnomad NFE AF: 0.557

Gnomad OTH AF: 0.577

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: 0.561 AC: 61762 AN: 110105 Hom.: 12332 Cov.: 23 AF XY: 0.556 AC XY: 18052 AN XY: 32443

African (AFR) AF: 0.577 AC: 17503 AN: 30359

American (AMR) AF: 0.541 AC: 5581 AN: 10323

Ashkenazi Jewish (ASJ) AF: 0.593 AC: 1558 AN: 2627

East Asian (EAS) AF: 0.554 AC: 1898 AN: 3429

South Asian (SAS) AF: 0.524 AC: 1383 AN: 2639

European-Finnish (FIN) AF: 0.569 AC: 3274 AN: 5757

Middle Eastern (MID) AF: 0.462 AC: 97 AN: 210

European-Non Finnish (NFE) AF: 0.557 AC: 29300 AN: 52587

Other (OTH) AF: 0.579 AC: 873 AN: 1508

Alfa AF: 0.556 Hom.: 4110

Bravo AF: 0.560

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	1.1
DANN	Benign	0.65
PhyloP100		-0.63

Splicing

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

Other links and lift over

dbSNP: rs1930674; hg19: chrX-144091597;