rs3845166

Positions:

• chr5-56404461-C-A

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 0.0761 in 152,242 control chromosomes in the GnomAD database, including 806 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 0.076 (806 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.162

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.177 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: 0.0760 AC: 11564 AN: 152124 Hom.: 807 Cov.: 32

Gnomad AFR AF: 0.176

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0369

Gnomad ASJ AF: 0.0294

Gnomad EAS AF: 0.187

Gnomad SAS AF: 0.0860

Gnomad FIN AF: 0.0167

Gnomad MID AF: 0.0633

Gnomad NFE AF: 0.0275

Gnomad OTH AF: 0.0684

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

GnomAD4 genome AF: 0.0761 AC: 11582 AN: 152242 Hom.: 806 Cov.: 32 AF XY: 0.0754 AC XY: 5611 AN XY: 74440

Gnomad4 AFR AF: 0.177

Gnomad4 AMR AF: 0.0367

Gnomad4 ASJ AF: 0.0294

Gnomad4 EAS AF: 0.186

Gnomad4 SAS AF: 0.0861

Gnomad4 FIN AF: 0.0167

Gnomad4 NFE AF: 0.0275

Gnomad4 OTH AF: 0.0691

Alfa AF: 0.0545 Hom.: 66

Bravo AF: 0.0818

Asia WGS AF: 0.130 AC: 449 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	1.3
DANN	Benign	0.56

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs3845166; hg19: chr5-55700288;