rs487359

Variant names:

• chr1-199412483-A-C
• rs487359

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 0.628 in 151,766 control chromosomes in the GnomAD database, including 30,295 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 0.63 (30295 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.186
• Publications: 3 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.03).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.677 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Frequencies

GnomAD3 genomes AF: 0.628 AC: 95289 AN: 151648 Hom.: 30269 Cov.: 33

Gnomad AFR AF: 0.684

Gnomad AMI AF: 0.770

Gnomad AMR AF: 0.662

Gnomad ASJ AF: 0.670

Gnomad EAS AF: 0.357

Gnomad SAS AF: 0.511

Gnomad FIN AF: 0.564

Gnomad MID AF: 0.703

Gnomad NFE AF: 0.622

Gnomad OTH AF: 0.640

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

GnomAD4 genome AF: 0.628 AC: 95362 AN: 151766 Hom.: 30295 Cov.: 33 AF XY: 0.623 AC XY: 46168 AN XY: 74154

African (AFR) AF: 0.683 AC: 28320 AN: 41446

American (AMR) AF: 0.662 AC: 10073 AN: 15220

Ashkenazi Jewish (ASJ) AF: 0.670 AC: 2320 AN: 3464

East Asian (EAS) AF: 0.358 AC: 1850 AN: 5170

South Asian (SAS) AF: 0.511 AC: 2463 AN: 4822

European-Finnish (FIN) AF: 0.564 AC: 5912 AN: 10478

Middle Eastern (MID) AF: 0.701 AC: 206 AN: 294

European-Non Finnish (NFE) AF: 0.622 AC: 42179 AN: 67858

Other (OTH) AF: 0.636 AC: 1338 AN: 2104

Alfa AF: 0.620 Hom.: 12137

Bravo AF: 0.639

Asia WGS AF: 0.424 AC: 1452 AN: 3414

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	1.8
DANN	Benign	0.37
PhyloP100		-0.19

Splicing

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

Other links and lift over

dbSNP: rs487359; hg19: chr1-199381611;