rs5987017

Variant names:

• chrX-153516714-A-G
• rs5987017

Your query was ambiguous. Multiple possible variants found:

• chrX-153516714-A-G
• chrX-153516714-A-T

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 0.78 (25174 hom., 25430 hem., cov: 23)
  • Failed GnomAD Quality Control
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.91
• Publications: 2 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).

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: 0.785 AC: 86310 AN: 110011 Hom.: 25180 Cov.: 23

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

African (AFR) AF: 0.497 AC: 15059 AN: 30274

American (AMR) AF: 0.822 AC: 8578 AN: 10439

Ashkenazi Jewish (ASJ) AF: 0.962 AC: 2526 AN: 2626

East Asian (EAS) AF: 0.744 AC: 2555 AN: 3433

South Asian (SAS) AF: 0.872 AC: 2143 AN: 2458

European-Finnish (FIN) AF: 0.910 AC: 5300 AN: 5826

Middle Eastern (MID) AF: 0.851 AC: 183 AN: 215

European-Non Finnish (NFE) AF: 0.917 AC: 48280 AN: 52636

Other (OTH) AF: 0.800 AC: 1191 AN: 1489

Alfa AF: 0.857 Hom.: 37378

Bravo AF: 0.764

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.16
DANN	Benign	0.51
PhyloP100		-1.9

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: rs5987017;

hg19: chrX-152782172;