X-71181867-A-T

Variant names:

• chrX-71181867-A-T
• rs5981084

Variant summary

Our verdict is Likely benign. Variant got -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 0.91 (32351 hom., 29801 hem., cov: 22)
  • Failed GnomAD Quality Control
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.248

ACMG classification

Verdict is Likely_benign. Variant got -4 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.74).

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: 0.910 AC: 100549 AN: 110484 Hom.: 32351 Cov.: 22 AF XY: 0.910 AC XY: 29737 AN XY: 32674

Gnomad AFR AF: 0.981

Gnomad AMI AF: 0.837

Gnomad AMR AF: 0.928

Gnomad ASJ AF: 0.924

Gnomad EAS AF: 0.999

Gnomad SAS AF: 0.988

Gnomad FIN AF: 0.806

Gnomad MID AF: 0.932

Gnomad NFE AF: 0.867

Gnomad OTH AF: 0.923

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: 0.910 AC: 100608 AN: 110537 Hom.: 32351 Cov.: 22 AF XY: 0.910 AC XY: 29801 AN XY: 32737

Gnomad4 AFR AF: 0.982

Gnomad4 AMR AF: 0.928

Gnomad4 ASJ AF: 0.924

Gnomad4 EAS AF: 0.999

Gnomad4 SAS AF: 0.987

Gnomad4 FIN AF: 0.806

Gnomad4 NFE AF: 0.867

Gnomad4 OTH AF: 0.924

Alfa AF: 0.897 Hom.: 7926

Bravo AF: 0.921

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.74
CADD	Benign	4.6
DANN	Benign	0.82

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs5981084; hg19: chrX-70401717;