rs5912838

Variant names:

• chrX-79241621-A-C
• rs5912838

Your query was ambiguous. Multiple possible variants found:

• chrX-79241621-A-C
• chrX-79241621-A-G

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 0.52 (11058 hom., 16947 hem., cov: 23)
  • Failed GnomAD Quality Control
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.848
• Publications: 9 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.81).

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: 0.522 AC: 57807 AN: 110684 Hom.: 11060 Cov.: 23

Gnomad AFR AF: 0.437

Gnomad AMI AF: 0.592

Gnomad AMR AF: 0.438

Gnomad ASJ AF: 0.501

Gnomad EAS AF: 0.392

Gnomad SAS AF: 0.430

Gnomad FIN AF: 0.613

Gnomad MID AF: 0.519

Gnomad NFE AF: 0.592

Gnomad OTH AF: 0.530

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: 0.522 AC: 57809 AN: 110736 Hom.: 11058 Cov.: 23 AF XY: 0.514 AC XY: 16947 AN XY: 33002

African (AFR) AF: 0.436 AC: 13299 AN: 30499

American (AMR) AF: 0.438 AC: 4607 AN: 10522

Ashkenazi Jewish (ASJ) AF: 0.501 AC: 1323 AN: 2639

East Asian (EAS) AF: 0.392 AC: 1386 AN: 3535

South Asian (SAS) AF: 0.429 AC: 1131 AN: 2635

European-Finnish (FIN) AF: 0.613 AC: 3549 AN: 5790

Middle Eastern (MID) AF: 0.523 AC: 113 AN: 216

European-Non Finnish (NFE) AF: 0.592 AC: 31209 AN: 52729

Other (OTH) AF: 0.530 AC: 794 AN: 1499

Alfa AF: 0.549 Hom.: 54575

Bravo AF: 0.502

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
CADD	Benign	6.3
DANN	Benign	0.87
PhyloP100		0.85

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs5912838; hg19: chrX-78497118;