rs486003

Variant names:

• chr1-181844634-A-G
• rs486003

Your query was ambiguous. Multiple possible variants found:

• chr1-181844634-A-G
• chr1-181844634-A-T

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 0.676 in 152,008 control chromosomes in the GnomAD database, including 34,967 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 0.68 (34967 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.815

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.757 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: 0.676 AC: 102656 AN: 151890 Hom.: 34938 Cov.: 32

Gnomad AFR AF: 0.603

Gnomad AMI AF: 0.656

Gnomad AMR AF: 0.671

Gnomad ASJ AF: 0.703

Gnomad EAS AF: 0.575

Gnomad SAS AF: 0.780

Gnomad FIN AF: 0.673

Gnomad MID AF: 0.756

Gnomad NFE AF: 0.720

Gnomad OTH AF: 0.690

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

GnomAD4 genome AF: 0.676 AC: 102736 AN: 152008 Hom.: 34967 Cov.: 32 AF XY: 0.675 AC XY: 50152 AN XY: 74290

Gnomad4 AFR AF: 0.603

Gnomad4 AMR AF: 0.671

Gnomad4 ASJ AF: 0.703

Gnomad4 EAS AF: 0.575

Gnomad4 SAS AF: 0.778

Gnomad4 FIN AF: 0.673

Gnomad4 NFE AF: 0.720

Gnomad4 OTH AF: 0.695

Alfa AF: 0.714 Hom.: 78015

Bravo AF: 0.669

Asia WGS AF: 0.673 AC: 2340 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.65
DANN	Benign	0.76

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs486003; hg19: chr1-181813769;