chr12-120600477-A-C

Position:

• chr12-120600477-A-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 0.267 in 151,988 control chromosomes in the GnomAD database, including 6,271 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 0.27 (6271 hom., cov: 32)
• Consequence: intergenic_region
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.467

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.459 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
		n.120600477A>C		intergenic_region

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.267 AC: 40572 AN: 151870 Hom.: 6259 Cov.: 32

Gnomad AFR AF: 0.116

Gnomad AMI AF: 0.245

Gnomad AMR AF: 0.281

Gnomad ASJ AF: 0.249

Gnomad EAS AF: 0.474

Gnomad SAS AF: 0.296

Gnomad FIN AF: 0.347

Gnomad MID AF: 0.253

Gnomad NFE AF: 0.328

Gnomad OTH AF: 0.258

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

GnomAD4 genome AF: 0.267 AC: 40599 AN: 151988 Hom.: 6271 Cov.: 32 AF XY: 0.271 AC XY: 20125 AN XY: 74304

Gnomad4 AFR AF: 0.116

Gnomad4 AMR AF: 0.282

Gnomad4 ASJ AF: 0.249

Gnomad4 EAS AF: 0.474

Gnomad4 SAS AF: 0.298

Gnomad4 FIN AF: 0.347

Gnomad4 NFE AF: 0.328

Gnomad4 OTH AF: 0.255

Alfa AF: 0.182 Hom.: 413

Bravo AF: 0.256

Asia WGS AF: 0.338 AC: 1177 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	1.9
DANN	Benign	0.41

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10774561; hg19: chr12-121038280;