3-55459486-C-A

Variant names:

• chr3-55459486-C-A
• rs476986

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 5 publications found

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	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

African (AFR) AF: 0.858 AC: 35607 AN: 41518

American (AMR) AF: 0.842 AC: 12892 AN: 15304

Ashkenazi Jewish (ASJ) AF: 0.793 AC: 2750 AN: 3470

East Asian (EAS) AF: 0.776 AC: 3987 AN: 5136

South Asian (SAS) AF: 0.824 AC: 3973 AN: 4822

European-Finnish (FIN) AF: 0.749 AC: 7922 AN: 10578

Middle Eastern (MID) AF: 0.782 AC: 230 AN: 294

European-Non Finnish (NFE) AF: 0.748 AC: 50875 AN: 68002

Other (OTH) AF: 0.792 AC: 1670 AN: 2108

Alfa AF: 0.767 Hom.: 185263

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
PhyloP100		0.48

Splicing

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

Other links and lift over

dbSNP: rs476986; hg19: chr3-55493514;