rs12132674

Positions:

• chr1-119778464-G-A

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 0.229 in 152,024 control chromosomes in the GnomAD database, including 4,266 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 0.23 (4266 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.277

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.282 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: 0.229 AC: 34811 AN: 151908 Hom.: 4262 Cov.: 32

Gnomad AFR AF: 0.181

Gnomad AMI AF: 0.281

Gnomad AMR AF: 0.165

Gnomad ASJ AF: 0.238

Gnomad EAS AF: 0.0405

Gnomad SAS AF: 0.201

Gnomad FIN AF: 0.251

Gnomad MID AF: 0.204

Gnomad NFE AF: 0.286

Gnomad OTH AF: 0.211

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

GnomAD4 genome AF: 0.229 AC: 34831 AN: 152024 Hom.: 4266 Cov.: 32 AF XY: 0.223 AC XY: 16579 AN XY: 74300

Gnomad4 AFR AF: 0.181

Gnomad4 AMR AF: 0.164

Gnomad4 ASJ AF: 0.238

Gnomad4 EAS AF: 0.0406

Gnomad4 SAS AF: 0.201

Gnomad4 FIN AF: 0.251

Gnomad4 NFE AF: 0.286

Gnomad4 OTH AF: 0.208

Alfa AF: 0.258 Hom.: 666

Bravo AF: 0.218

Asia WGS AF: 0.152 AC: 529 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	1.2
DANN	Benign	0.36

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs12132674; hg19: chr1-120321087;