rs476986

Positions:

• chr3-55459486-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 0.793 in 152,144 control chromosomes in the GnomAD database, including 48,016 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 0.79 (48016 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.485

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.85 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: 0.793 AC: 120612 AN: 152026 Hom.: 47992 Cov.: 32

Gnomad AFR AF: 0.858

Gnomad AMI AF: 0.848

Gnomad AMR AF: 0.842

Gnomad ASJ AF: 0.793

Gnomad EAS AF: 0.777

Gnomad SAS AF: 0.825

Gnomad FIN AF: 0.749

Gnomad MID AF: 0.782

Gnomad NFE AF: 0.748

Gnomad OTH AF: 0.797

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

GnomAD4 genome AF: 0.793 AC: 120679 AN: 152144 Hom.: 48016 Cov.: 32 AF XY: 0.793 AC XY: 58966 AN XY: 74368

Gnomad4 AFR AF: 0.858

Gnomad4 AMR AF: 0.842

Gnomad4 ASJ AF: 0.793

Gnomad4 EAS AF: 0.776

Gnomad4 SAS AF: 0.824

Gnomad4 FIN AF: 0.749

Gnomad4 NFE AF: 0.748

Gnomad4 OTH AF: 0.792

Alfa AF: 0.763 Hom.: 78595

Bravo AF: 0.803

Asia WGS AF: 0.806 AC: 2802 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	5.1
DANN	Benign	0.29

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs476986; hg19: chr3-55493514;