X-146271035-T-C

Variant names:

• chrX-146271035-T-C
• rs5920061

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 0.59 (14117 hom., 19321 hem., cov: 23)
  • Failed GnomAD Quality Control
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.542
• Publications: 2 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).

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: 0.594 AC: 65802 AN: 110750 Hom.: 14128 Cov.: 23

Gnomad AFR AF: 0.657

Gnomad AMI AF: 0.462

Gnomad AMR AF: 0.455

Gnomad ASJ AF: 0.571

Gnomad EAS AF: 0.690

Gnomad SAS AF: 0.595

Gnomad FIN AF: 0.546

Gnomad MID AF: 0.572

Gnomad NFE AF: 0.588

Gnomad OTH AF: 0.571

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: 0.594 AC: 65801 AN: 110799 Hom.: 14117 Cov.: 23 AF XY: 0.584 AC XY: 19321 AN XY: 33073

African (AFR) AF: 0.657 AC: 19963 AN: 30398

American (AMR) AF: 0.454 AC: 4758 AN: 10482

Ashkenazi Jewish (ASJ) AF: 0.571 AC: 1500 AN: 2626

East Asian (EAS) AF: 0.690 AC: 2396 AN: 3472

South Asian (SAS) AF: 0.591 AC: 1550 AN: 2622

European-Finnish (FIN) AF: 0.546 AC: 3239 AN: 5935

Middle Eastern (MID) AF: 0.553 AC: 119 AN: 215

European-Non Finnish (NFE) AF: 0.588 AC: 31102 AN: 52853

Other (OTH) AF: 0.567 AC: 862 AN: 1520

Alfa AF: 0.582 Hom.: 22345

Bravo AF: 0.586

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.52
DANN	Benign	0.37
PhyloP100		-0.54

Splicing

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

Other links and lift over

dbSNP: rs5920061; hg19: chrX-145352553;