5-56683302-A-C

Position:

• chr5-56683302-A-C

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 0.285 in 151,962 control chromosomes in the GnomAD database, including 6,701 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 0.29 (6701 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.899

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.81).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.394 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.285 AC: 43337 AN: 151844 Hom.: 6691 Cov.: 32

Gnomad AFR AF: 0.399

Gnomad AMI AF: 0.216

Gnomad AMR AF: 0.353

Gnomad ASJ AF: 0.238

Gnomad EAS AF: 0.237

Gnomad SAS AF: 0.276

Gnomad FIN AF: 0.217

Gnomad MID AF: 0.326

Gnomad NFE AF: 0.219

Gnomad OTH AF: 0.294

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

GnomAD4 genome AF: 0.285 AC: 43375 AN: 151962 Hom.: 6701 Cov.: 32 AF XY: 0.287 AC XY: 21355 AN XY: 74288

Gnomad4 AFR AF: 0.399

Gnomad4 AMR AF: 0.354

Gnomad4 ASJ AF: 0.238

Gnomad4 EAS AF: 0.237

Gnomad4 SAS AF: 0.276

Gnomad4 FIN AF: 0.217

Gnomad4 NFE AF: 0.219

Gnomad4 OTH AF: 0.291

Alfa AF: 0.249 Hom.: 2318

Bravo AF: 0.305

Asia WGS AF: 0.224 AC: 779 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
CADD	Benign	4.2
DANN	Benign	0.74

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs13362504; hg19: chr5-55979129;