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).

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: 0.522 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 v4.3

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

Other links and lift over

dbSNP: rs5912838; hg19: chrX-78497118;