rs12084280

Positions:

• chr1-162054019-G-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 0.192 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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	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;