12-60664785-G-C

Variant names:

• chr12-60664785-G-C
• rs1909255

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 0.0844 in 151,416 control chromosomes in the GnomAD database, including 1,180 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 0.084 (1180 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.06
• Publications: 0 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.281 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: 0.0842 AC: 12743 AN: 151296 Hom.: 1174 Cov.: 32

Gnomad AFR AF: 0.204

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0607

Gnomad ASJ AF: 0.00841

Gnomad EAS AF: 0.293

Gnomad SAS AF: 0.0762

Gnomad FIN AF: 0.0284

Gnomad MID AF: 0.0190

Gnomad NFE AF: 0.0156

Gnomad OTH AF: 0.0554

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

GnomAD4 genome AF: 0.0844 AC: 12783 AN: 151416 Hom.: 1180 Cov.: 32 AF XY: 0.0851 AC XY: 6301 AN XY: 74008

African (AFR) AF: 0.205 AC: 8476 AN: 41412

American (AMR) AF: 0.0608 AC: 922 AN: 15166

Ashkenazi Jewish (ASJ) AF: 0.00841 AC: 29 AN: 3450

East Asian (EAS) AF: 0.293 AC: 1512 AN: 5158

South Asian (SAS) AF: 0.0764 AC: 369 AN: 4828

European-Finnish (FIN) AF: 0.0284 AC: 300 AN: 10570

Middle Eastern (MID) AF: 0.0238 AC: 7 AN: 294

European-Non Finnish (NFE) AF: 0.0156 AC: 1054 AN: 67528

Other (OTH) AF: 0.0543 AC: 114 AN: 2098

Alfa AF: 0.0508 Hom.: 70

Bravo AF: 0.0927

Asia WGS AF: 0.188 AC: 654 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	0.71
DANN	Benign	0.70
PhyloP100		-1.1

Splicing

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

Other links and lift over

dbSNP: rs1909255; hg19: chr12-61058566;