chrX-5561570-C-A

Variant names:

• chrX-5561570-C-A
• rs5916144

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 0.74 (21260 hom., 24159 hem., cov: 23)
  • Failed GnomAD Quality Control
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.664
• 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=-0.99).

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: 0.738 AC: 81451 AN: 110352 Hom.: 21261 Cov.: 23

Gnomad AFR AF: 0.733

Gnomad AMI AF: 0.781

Gnomad AMR AF: 0.826

Gnomad ASJ AF: 0.719

Gnomad EAS AF: 0.876

Gnomad SAS AF: 0.605

Gnomad FIN AF: 0.780

Gnomad MID AF: 0.582

Gnomad NFE AF: 0.718

Gnomad OTH AF: 0.732

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: 0.738 AC: 81489 AN: 110406 Hom.: 21260 Cov.: 23 AF XY: 0.740 AC XY: 24159 AN XY: 32636

African (AFR) AF: 0.733 AC: 22194 AN: 30286

American (AMR) AF: 0.826 AC: 8560 AN: 10363

Ashkenazi Jewish (ASJ) AF: 0.719 AC: 1893 AN: 2634

East Asian (EAS) AF: 0.876 AC: 3040 AN: 3469

South Asian (SAS) AF: 0.604 AC: 1549 AN: 2563

European-Finnish (FIN) AF: 0.780 AC: 4577 AN: 5865

Middle Eastern (MID) AF: 0.583 AC: 126 AN: 216

European-Non Finnish (NFE) AF: 0.718 AC: 37929 AN: 52826

Other (OTH) AF: 0.725 AC: 1094 AN: 1509

Alfa AF: 0.724 Hom.: 90867

Bravo AF: 0.747

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	1.1
DANN	Benign	0.32
PhyloP100		-0.66

Splicing

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

Other links and lift over

dbSNP: rs5916144; hg19: chrX-5479611;