5-70009930-A-G

Variant names:

• chr5-70009930-A-G
• rs27503

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 0.41 (413 hom., cov: 11)
  • Failed GnomAD Quality Control
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.62
• Publications: 0 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).

Variant Effect in Transcripts

 

RefSeq Transcripts

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

Ensembl Transcripts

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

Frequencies

GnomAD3 genomes AF: 0.411 AC: 30356 AN: 73890 Hom.: 412 Cov.: 11

Gnomad AFR AF: 0.390

Gnomad AMI AF: 0.381

Gnomad AMR AF: 0.430

Gnomad ASJ AF: 0.328

Gnomad EAS AF: 0.465

Gnomad SAS AF: 0.413

Gnomad FIN AF: 0.423

Gnomad MID AF: 0.352

Gnomad NFE AF: 0.414

Gnomad OTH AF: 0.387

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: AS_VQSR;InbreedingCoeff AF: 0.411 AC: 30366 AN: 73912 Hom.: 413 Cov.: 11 AF XY: 0.407 AC XY: 14055 AN XY: 34568

⚠️ The allele balance in gnomAD version 4 Genomes is significantly skewed from the expected value of 0.5.

African (AFR) AF: 0.390 AC: 5346 AN: 13692

American (AMR) AF: 0.430 AC: 3058 AN: 7112

Ashkenazi Jewish (ASJ) AF: 0.328 AC: 650 AN: 1984

East Asian (EAS) AF: 0.465 AC: 1544 AN: 3322

South Asian (SAS) AF: 0.412 AC: 1000 AN: 2426

European-Finnish (FIN) AF: 0.423 AC: 1956 AN: 4628

Middle Eastern (MID) AF: 0.345 AC: 67 AN: 194

European-Non Finnish (NFE) AF: 0.414 AC: 16165 AN: 39050

Other (OTH) AF: 0.388 AC: 388 AN: 1000

⚠️ The allele balance in gnomAD version 4 Genomes is significantly skewed from the expected value of 0.5. (p-value = 0), which strongly suggests a high chance of mosaicism in these individuals.

Alfa AF: 0.374 Hom.: 342

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.95
DANN	Benign	0.52
PhyloP100		-1.6

Splicing

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

Other links and lift over

dbSNP: rs27503; hg19: chr5-69305757;