rs5905587

chrX-43974750-T-CchrX-43974750-T-G

Variant summary

Our verdict is Benign. Variant got -8 ACMG points: 0P and 8B. BP4_Strong BS2

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 0.60 (14669 hom., 18715 hem., cov: 22)
  • Failed GnomAD Quality Control
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.30

ACMG classification

Verdict is Benign. Variant got -8 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BS2: High Homozygotes in GnomAd at 14662 gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.603 AC: 65882 AN: 109319 Hom.: 14662 Cov.: 22 AF XY: 0.591 AC XY: 18677 AN XY: 31617

Gnomad AFR AF: 0.629

Gnomad AMI AF: 0.613

Gnomad AMR AF: 0.526

Gnomad ASJ AF: 0.618

Gnomad EAS AF: 0.334

Gnomad SAS AF: 0.338

Gnomad FIN AF: 0.660

Gnomad MID AF: 0.476

Gnomad NFE AF: 0.627

Gnomad OTH AF: 0.581

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: 0.603 AC: 65926 AN: 109367 Hom.: 14669 Cov.: 22 AF XY: 0.591 AC XY: 18715 AN XY: 31675

Gnomad4 AFR AF: 0.629

Gnomad4 AMR AF: 0.526

Gnomad4 ASJ AF: 0.618

Gnomad4 EAS AF: 0.334

Gnomad4 SAS AF: 0.339

Gnomad4 FIN AF: 0.660

Gnomad4 NFE AF: 0.627

Gnomad4 OTH AF: 0.576

Alfa AF: 0.615 Hom.: 65357

Bravo AF: 0.600

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
Cadd	Benign	0.69
Dann	Benign	0.34

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs5905587; hg19: chrX-43833996;