5-132683291-G-C

Variant names:

• chr5-132683291-G-C
• rs2243291

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The variant allele was found at a frequency of 0.335 in 152,052 control chromosomes in the GnomAD database, including 11,905 homozygotes. 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 0.34 (11905 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.214

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.756 is higher than 0.05.

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: 0.335 AC: 50886 AN: 151934 Hom.: 11874 Cov.: 32

Gnomad AFR AF: 0.601

Gnomad AMI AF: 0.0165

Gnomad AMR AF: 0.338

Gnomad ASJ AF: 0.206

Gnomad EAS AF: 0.777

Gnomad SAS AF: 0.195

Gnomad FIN AF: 0.363

Gnomad MID AF: 0.171

Gnomad NFE AF: 0.157

Gnomad OTH AF: 0.293

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.335 AC: 50977 AN: 152052 Hom.: 11905 Cov.: 32 AF XY: 0.342 AC XY: 25425 AN XY: 74300

Gnomad4 AFR AF: 0.601

Gnomad4 AMR AF: 0.338

Gnomad4 ASJ AF: 0.206

Gnomad4 EAS AF: 0.776

Gnomad4 SAS AF: 0.195

Gnomad4 FIN AF: 0.363

Gnomad4 NFE AF: 0.157

Gnomad4 OTH AF: 0.296

Alfa AF: 0.124 Hom.: 243

Bravo AF: 0.352

Asia WGS AF: 0.484 AC: 1683 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	5.9
DANN	Benign	0.29

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2243291; hg19: chr5-132018983;