rs12084280

Variant names:

• chr1-162054019-G-C
• rs12084280

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 0.192 in 152,122 control chromosomes in the GnomAD database, including 4,183 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 0.19 (4183 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.421

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.386 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: 0.192 AC: 29204 AN: 152004 Hom.: 4174 Cov.: 32

Gnomad AFR AF: 0.390

Gnomad AMI AF: 0.0888

Gnomad AMR AF: 0.160

Gnomad ASJ AF: 0.0775

Gnomad EAS AF: 0.349

Gnomad SAS AF: 0.184

Gnomad FIN AF: 0.117

Gnomad MID AF: 0.101

Gnomad NFE AF: 0.0876

Gnomad OTH AF: 0.170

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

GnomAD4 genome AF: 0.192 AC: 29247 AN: 152122 Hom.: 4183 Cov.: 32 AF XY: 0.192 AC XY: 14305 AN XY: 74380

Gnomad4 AFR AF: 0.391

Gnomad4 AMR AF: 0.160

Gnomad4 ASJ AF: 0.0775

Gnomad4 EAS AF: 0.349

Gnomad4 SAS AF: 0.182

Gnomad4 FIN AF: 0.117

Gnomad4 NFE AF: 0.0876

Gnomad4 OTH AF: 0.169

Alfa AF: 0.142 Hom.: 300

Bravo AF: 0.203

Asia WGS AF: 0.275 AC: 954 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	7.4
DANN	Benign	0.75

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs12084280; hg19: chr1-162023809;