rs5981088

Variant names:

• chrX-71199915-A-G
• rs5981088

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 0.56 (12736 hom., 18077 hem., cov: 23)
  • Failed GnomAD Quality Control
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.239
• Publications: 1 publications found

ACMG classification

Our verdict: Likely_benign. The variant received -4 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).

Variant Effect in Transcripts

 

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Frequencies

GnomAD3 genomes AF: 0.557 AC: 61477 AN: 110374 Hom.: 12724 Cov.: 23

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

African (AFR) AF: 0.695 AC: 21055 AN: 30284

American (AMR) AF: 0.627 AC: 6429 AN: 10255

Ashkenazi Jewish (ASJ) AF: 0.650 AC: 1716 AN: 2642

East Asian (EAS) AF: 0.747 AC: 2610 AN: 3494

South Asian (SAS) AF: 0.584 AC: 1536 AN: 2630

European-Finnish (FIN) AF: 0.416 AC: 2438 AN: 5865

Middle Eastern (MID) AF: 0.647 AC: 139 AN: 215

European-Non Finnish (NFE) AF: 0.459 AC: 24261 AN: 52857

Other (OTH) AF: 0.603 AC: 911 AN: 1512

Alfa AF: 0.512 Hom.: 58966

Bravo AF: 0.581

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	1.2
DANN	Benign	0.44
PhyloP100		-0.24

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs5981088;

hg19: chrX-70419765;