rs5987017

chrX-153516714-A-GchrX-153516714-A-T

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 0.78 (25174 hom., 25430 hem., cov: 23)
  • Failed GnomAD Quality Control
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.91

ACMG classification

Verdict is Benign. Variant got -8 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BS2: High Homozygotes in GnomAd at 25180 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: 0.785 AC: 86310 AN: 110011 Hom.: 25180 Cov.: 23 AF XY: 0.786 AC XY: 25385 AN XY: 32295

Gnomad AFR AF: 0.497

Gnomad AMI AF: 0.789

Gnomad AMR AF: 0.822

Gnomad ASJ AF: 0.962

Gnomad EAS AF: 0.743

Gnomad SAS AF: 0.871

Gnomad FIN AF: 0.910

Gnomad MID AF: 0.857

Gnomad NFE AF: 0.917

Gnomad OTH AF: 0.797

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: 0.784 AC: 86342 AN: 110064 Hom.: 25174 Cov.: 23 AF XY: 0.786 AC XY: 25430 AN XY: 32358

Gnomad4 AFR AF: 0.497

Gnomad4 AMR AF: 0.822

Gnomad4 ASJ AF: 0.962

Gnomad4 EAS AF: 0.744

Gnomad4 SAS AF: 0.872

Gnomad4 FIN AF: 0.910

Gnomad4 NFE AF: 0.917

Gnomad4 OTH AF: 0.800

Alfa AF: 0.881 Hom.: 25777

Bravo AF: 0.764

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
Cadd	Benign	0.16
Dann	Benign	0.51

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs5987017; hg19: chrX-152782172;