rs487359

Positions:

• chr1-199412483-A-C

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 0.628 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

ACMG classification

Verdict is Benign. Variant got -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.

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: 0.628 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

Gnomad4 AFR AF: 0.683

Gnomad4 AMR AF: 0.662

Gnomad4 ASJ AF: 0.670

Gnomad4 EAS AF: 0.358

Gnomad4 SAS AF: 0.511

Gnomad4 FIN AF: 0.564

Gnomad4 NFE AF: 0.622

Gnomad4 OTH AF: 0.636

Alfa AF: 0.619 Hom.: 10905

Bravo AF: 0.639

Asia WGS AF: 0.424 AC: 1452 AN: 3414

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs487359; hg19: chr1-199381611;