5-56028975-A-C

Position:

• chr5-56028975-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 0.189 in 152,108 control chromosomes in the GnomAD database, including 2,783 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 0.19 (2783 hom., cov: 32)
• Consequence: intergenic_region
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.68

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.245 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
		n.56028975A>C		intergenic_region

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ENSG00000249236	ENST00000645512.1	n.279+34774A>C		intron_variant

Frequencies

GnomAD3 genomes AF: 0.189 AC: 28686 AN: 151990 Hom.: 2779 Cov.: 32

Gnomad AFR AF: 0.188

Gnomad AMI AF: 0.221

Gnomad AMR AF: 0.168

Gnomad ASJ AF: 0.209

Gnomad EAS AF: 0.0627

Gnomad SAS AF: 0.257

Gnomad FIN AF: 0.180

Gnomad MID AF: 0.215

Gnomad NFE AF: 0.198

Gnomad OTH AF: 0.205

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

GnomAD4 genome AF: 0.189 AC: 28710 AN: 152108 Hom.: 2783 Cov.: 32 AF XY: 0.185 AC XY: 13797 AN XY: 74386

Gnomad4 AFR AF: 0.188

Gnomad4 AMR AF: 0.168

Gnomad4 ASJ AF: 0.209

Gnomad4 EAS AF: 0.0626

Gnomad4 SAS AF: 0.257

Gnomad4 FIN AF: 0.180

Gnomad4 NFE AF: 0.198

Gnomad4 OTH AF: 0.204

Alfa AF: 0.198 Hom.: 1795

Bravo AF: 0.186

Asia WGS AF: 0.158 AC: 551 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	5.8
DANN	Benign	0.79

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs16884711; hg19: chr5-55324802;