chr12-60727464-A-G

Variant names:

• chr12-60727464-A-G
• rs273849

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 0.355 in 151,796 control chromosomes in the GnomAD database, including 14,907 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 0.36 (14907 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.13
• Publications: 5 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.03).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.768 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Frequencies

GnomAD3 genomes AF: 0.355 AC: 53851 AN: 151676 Hom.: 14858 Cov.: 31

Gnomad AFR AF: 0.775

Gnomad AMI AF: 0.218

Gnomad AMR AF: 0.321

Gnomad ASJ AF: 0.139

Gnomad EAS AF: 0.207

Gnomad SAS AF: 0.189

Gnomad FIN AF: 0.179

Gnomad MID AF: 0.231

Gnomad NFE AF: 0.173

Gnomad OTH AF: 0.301

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

GnomAD4 genome AF: 0.355 AC: 53958 AN: 151796 Hom.: 14907 Cov.: 31 AF XY: 0.351 AC XY: 26084 AN XY: 74220

African (AFR) AF: 0.776 AC: 32078 AN: 41364

American (AMR) AF: 0.321 AC: 4890 AN: 15214

Ashkenazi Jewish (ASJ) AF: 0.139 AC: 482 AN: 3462

East Asian (EAS) AF: 0.208 AC: 1066 AN: 5136

South Asian (SAS) AF: 0.189 AC: 910 AN: 4820

European-Finnish (FIN) AF: 0.179 AC: 1898 AN: 10586

Middle Eastern (MID) AF: 0.238 AC: 70 AN: 294

European-Non Finnish (NFE) AF: 0.173 AC: 11740 AN: 67904

Other (OTH) AF: 0.297 AC: 626 AN: 2108

Alfa AF: 0.126 Hom.: 297

Bravo AF: 0.388

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.61
DANN	Benign	0.42
PhyloP100		-1.1

Splicing

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

Other links and lift over

dbSNP: rs273849; hg19: chr12-61121245;