rs666282

Variant names:

• chr1-187927074-C-A
• rs666282

Your query was ambiguous. Multiple possible variants found:

• chr1-187927074-C-A
• chr1-187927074-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 0.782 in 152,070 control chromosomes in the GnomAD database, including 46,825 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 0.78 (46825 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.339
• Publications: 1 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.828 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: 0.781 AC: 118739 AN: 151952 Hom.: 46780 Cov.: 32

Gnomad AFR AF: 0.835

Gnomad AMI AF: 0.855

Gnomad AMR AF: 0.712

Gnomad ASJ AF: 0.805

Gnomad EAS AF: 0.512

Gnomad SAS AF: 0.761

Gnomad FIN AF: 0.760

Gnomad MID AF: 0.832

Gnomad NFE AF: 0.787

Gnomad OTH AF: 0.790

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

GnomAD4 genome AF: 0.782 AC: 118846 AN: 152070 Hom.: 46825 Cov.: 32 AF XY: 0.778 AC XY: 57788 AN XY: 74320

African (AFR) AF: 0.835 AC: 34648 AN: 41492

American (AMR) AF: 0.712 AC: 10873 AN: 15266

Ashkenazi Jewish (ASJ) AF: 0.805 AC: 2794 AN: 3472

East Asian (EAS) AF: 0.512 AC: 2637 AN: 5146

South Asian (SAS) AF: 0.761 AC: 3670 AN: 4824

European-Finnish (FIN) AF: 0.760 AC: 8039 AN: 10574

Middle Eastern (MID) AF: 0.827 AC: 243 AN: 294

European-Non Finnish (NFE) AF: 0.787 AC: 53489 AN: 67980

Other (OTH) AF: 0.793 AC: 1673 AN: 2110

Alfa AF: 0.778 Hom.: 7508

Bravo AF: 0.777

Asia WGS AF: 0.665 AC: 2311 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.77
DANN	Benign	0.35
PhyloP100		-0.34

Splicing

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

Other links and lift over

dbSNP: rs666282; hg19: chr1-187896205;