rs645486

Variant names:

• chr3-55458298-C-A
• rs645486

Your query was ambiguous. Multiple possible variants found:

• chr3-55458298-C-A
• chr3-55458298-C-G
• chr3-55458298-C-T

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 0.798 in 152,172 control chromosomes in the GnomAD database, including 48,671 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 0.80 (48671 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.790
• Publications: 5 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.868 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: 0.798 AC: 121395 AN: 152056 Hom.: 48646 Cov.: 33

Gnomad AFR AF: 0.876

Gnomad AMI AF: 0.848

Gnomad AMR AF: 0.844

Gnomad ASJ AF: 0.793

Gnomad EAS AF: 0.776

Gnomad SAS AF: 0.825

Gnomad FIN AF: 0.749

Gnomad MID AF: 0.782

Gnomad NFE AF: 0.748

Gnomad OTH AF: 0.798

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

GnomAD4 genome AF: 0.798 AC: 121464 AN: 152172 Hom.: 48671 Cov.: 33 AF XY: 0.798 AC XY: 59344 AN XY: 74368

African (AFR) AF: 0.875 AC: 36345 AN: 41530

American (AMR) AF: 0.844 AC: 12907 AN: 15298

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

East Asian (EAS) AF: 0.775 AC: 3984 AN: 5142

South Asian (SAS) AF: 0.824 AC: 3974 AN: 4820

European-Finnish (FIN) AF: 0.749 AC: 7931 AN: 10586

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

European-Non Finnish (NFE) AF: 0.748 AC: 50892 AN: 68004

Other (OTH) AF: 0.793 AC: 1678 AN: 2116

Alfa AF: 0.761 Hom.: 5398

Bravo AF: 0.809

Asia WGS AF: 0.808 AC: 2809 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.079
DANN	Benign	0.47
PhyloP100		-0.79

Splicing

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

Other links and lift over

dbSNP: rs645486; hg19: chr3-55492326;