rs27503

Variant names:

• chr5-70009930-A-G
• rs27503

Your query was ambiguous. Multiple possible variants found:

• chr5-70009930-A-G
• chr5-70009930-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 0.41 (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).

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: 0.411 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 v4.3

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;