rs5930817

Variant names:

• chrX-135916114-G-A
• rs5930817

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 0.99 (37791 hom., 32247 hem., cov: 22)
  • Failed GnomAD Quality Control
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.45
• 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=-1.02).

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: 0.986 AC: 108868 AN: 110464 Hom.: 37795 Cov.: 22

Gnomad AFR AF: 0.951

Gnomad AMI AF: 1.00

Gnomad AMR AF: 0.995

Gnomad ASJ AF: 1.00

Gnomad EAS AF: 1.00

Gnomad SAS AF: 1.00

Gnomad FIN AF: 1.00

Gnomad MID AF: 1.00

Gnomad NFE AF: 0.999

Gnomad OTH AF: 0.984

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: 0.986 AC: 108915 AN: 110517 Hom.: 37791 Cov.: 22 AF XY: 0.986 AC XY: 32247 AN XY: 32699

African (AFR) AF: 0.951 AC: 28843 AN: 30331

American (AMR) AF: 0.995 AC: 10293 AN: 10347

Ashkenazi Jewish (ASJ) AF: 1.00 AC: 2635 AN: 2635

East Asian (EAS) AF: 1.00 AC: 3490 AN: 3490

South Asian (SAS) AF: 1.00 AC: 2544 AN: 2544

European-Finnish (FIN) AF: 1.00 AC: 5850 AN: 5850

Middle Eastern (MID) AF: 1.00 AC: 217 AN: 217

European-Non Finnish (NFE) AF: 0.999 AC: 52880 AN: 52917

Other (OTH) AF: 0.985 AC: 1477 AN: 1500

Alfa AF: 0.991 Hom.: 10488

Bravo AF: 0.983

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.62
DANN	Benign	0.29
PhyloP100		-1.4

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: rs5930817;

hg19: chrX-134998273;