5-56810169-A-G

Position:

• chr5-56810169-A-G

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 0.0577 in 152,308 control chromosomes in the GnomAD database, including 355 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 0.058 (355 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.108

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 (SAS) allele frequency at 95% confidence interval = 0.143 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.0577 AC: 8786 AN: 152190 Hom.: 355 Cov.: 33

Gnomad AFR AF: 0.0137

Gnomad AMI AF: 0.0800

Gnomad AMR AF: 0.0486

Gnomad ASJ AF: 0.0885

Gnomad EAS AF: 0.0150

Gnomad SAS AF: 0.151

Gnomad FIN AF: 0.0664

Gnomad MID AF: 0.101

Gnomad NFE AF: 0.0798

Gnomad OTH AF: 0.0612

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

GnomAD4 genome AF: 0.0577 AC: 8788 AN: 152308 Hom.: 355 Cov.: 33 AF XY: 0.0597 AC XY: 4446 AN XY: 74472

Gnomad4 AFR AF: 0.0136

Gnomad4 AMR AF: 0.0485

Gnomad4 ASJ AF: 0.0885

Gnomad4 EAS AF: 0.0150

Gnomad4 SAS AF: 0.152

Gnomad4 FIN AF: 0.0664

Gnomad4 NFE AF: 0.0798

Gnomad4 OTH AF: 0.0597

Alfa AF: 0.0715 Hom.: 148

Bravo AF: 0.0519

Asia WGS AF: 0.0790 AC: 274 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	3.6
DANN	Benign	0.31

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs17661089; hg19: chr5-56105996;