X-44055387-T-C

Variant names:

• chrX-44055387-T-C
• rs1375329

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 0.78 (23928 hom., 25659 hem., cov: 23)
  • Failed GnomAD Quality Control
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.65
• Publications: 5 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.65).

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: 0.782 AC: 86489 AN: 110613 Hom.: 23938 Cov.: 23

Gnomad AFR AF: 0.860

Gnomad AMI AF: 0.647

Gnomad AMR AF: 0.785

Gnomad ASJ AF: 0.752

Gnomad EAS AF: 0.895

Gnomad SAS AF: 0.809

Gnomad FIN AF: 0.720

Gnomad MID AF: 0.689

Gnomad NFE AF: 0.738

Gnomad OTH AF: 0.788

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: 0.782 AC: 86537 AN: 110671 Hom.: 23928 Cov.: 23 AF XY: 0.781 AC XY: 25659 AN XY: 32871

African (AFR) AF: 0.860 AC: 26177 AN: 30424

American (AMR) AF: 0.785 AC: 8138 AN: 10369

Ashkenazi Jewish (ASJ) AF: 0.752 AC: 1975 AN: 2628

East Asian (EAS) AF: 0.895 AC: 3134 AN: 3503

South Asian (SAS) AF: 0.809 AC: 2119 AN: 2620

European-Finnish (FIN) AF: 0.720 AC: 4193 AN: 5826

Middle Eastern (MID) AF: 0.679 AC: 146 AN: 215

European-Non Finnish (NFE) AF: 0.738 AC: 39035 AN: 52903

Other (OTH) AF: 0.785 AC: 1181 AN: 1504

Alfa AF: 0.760 Hom.: 81181

Bravo AF: 0.793

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.65
CADD	Benign	4.2
DANN	Benign	0.64
PhyloP100		-1.7

Splicing

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

Other links and lift over

dbSNP: rs1375329; hg19: chrX-43914633;