12-120600477-A-C

Variant names:

• chr12-120600477-A-C
• rs10774561

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 0.267 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: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.467
• Publications: 9 publications found

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	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

African (AFR) AF: 0.116 AC: 4799 AN: 41454

American (AMR) AF: 0.282 AC: 4303 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.249 AC: 864 AN: 3472

East Asian (EAS) AF: 0.474 AC: 2446 AN: 5158

South Asian (SAS) AF: 0.298 AC: 1435 AN: 4808

European-Finnish (FIN) AF: 0.347 AC: 3666 AN: 10568

Middle Eastern (MID) AF: 0.248 AC: 73 AN: 294

European-Non Finnish (NFE) AF: 0.328 AC: 22254 AN: 67948

Other (OTH) AF: 0.255 AC: 536 AN: 2104

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 v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	1.9
DANN	Benign	0.41
PhyloP100		-0.47

Splicing

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

Other links and lift over

dbSNP: rs10774561; hg19: chr12-121038280;