chr5-132683291-G-C

Variant names:

• chr5-132683291-G-C
• rs2243291

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 18 publications found

ACMG classification

Our verdict: Benign. The variant received -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.

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: 0.335 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

African (AFR) AF: 0.601 AC: 24916 AN: 41464

American (AMR) AF: 0.338 AC: 5163 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.206 AC: 714 AN: 3464

East Asian (EAS) AF: 0.776 AC: 4019 AN: 5178

South Asian (SAS) AF: 0.195 AC: 938 AN: 4818

European-Finnish (FIN) AF: 0.363 AC: 3830 AN: 10544

Middle Eastern (MID) AF: 0.180 AC: 53 AN: 294

European-Non Finnish (NFE) AF: 0.157 AC: 10704 AN: 67990

Other (OTH) AF: 0.296 AC: 625 AN: 2114

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 v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	5.9
DANN	Benign	0.29
PhyloP100		0.21

Splicing

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

Other links and lift over

dbSNP: rs2243291; hg19: chr5-132018983;