rs5981088

chrX-71199915-A-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 0.56 (12736 hom., 18077 hem., cov: 23)
  • Failed GnomAD Quality Control
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.239

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 12724 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: 0.557 AC: 61477 AN: 110374 Hom.: 12724 Cov.: 23 AF XY: 0.552 AC XY: 18032 AN XY: 32678

Gnomad AFR AF: 0.695

Gnomad AMI AF: 0.650

Gnomad AMR AF: 0.627

Gnomad ASJ AF: 0.650

Gnomad EAS AF: 0.747

Gnomad SAS AF: 0.585

Gnomad FIN AF: 0.416

Gnomad MID AF: 0.633

Gnomad NFE AF: 0.459

Gnomad OTH AF: 0.595

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: 0.557 AC: 61534 AN: 110429 Hom.: 12736 Cov.: 23 AF XY: 0.552 AC XY: 18077 AN XY: 32743

Gnomad4 AFR AF: 0.695

Gnomad4 AMR AF: 0.627

Gnomad4 ASJ AF: 0.650

Gnomad4 EAS AF: 0.747

Gnomad4 SAS AF: 0.584

Gnomad4 FIN AF: 0.416

Gnomad4 NFE AF: 0.459

Gnomad4 OTH AF: 0.603

Alfa AF: 0.491 Hom.: 40887

Bravo AF: 0.581

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
Cadd	Benign	1.2
Dann	Benign	0.44

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs5981088; hg19: chrX-70419765;