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).

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: 0.785 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 v4.3

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

Other links and lift over

dbSNP: rs5987017; hg19: chrX-152782172;