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).

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: 0.561 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 v4.3

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;