chr12-67162339-A-G

Variant names:

• chr12-67162339-A-G
• rs1405467

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 0.606 in 151,978 control chromosomes in the GnomAD database, including 32,707 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 0.61 (32707 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.484
• Publications: 3 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 = 0.894 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.607 AC: 92112 AN: 151860 Hom.: 32699 Cov.: 31

Gnomad AFR AF: 0.209

Gnomad AMI AF: 0.822

Gnomad AMR AF: 0.762

Gnomad ASJ AF: 0.734

Gnomad EAS AF: 0.916

Gnomad SAS AF: 0.835

Gnomad FIN AF: 0.706

Gnomad MID AF: 0.672

Gnomad NFE AF: 0.747

Gnomad OTH AF: 0.662

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

GnomAD4 genome AF: 0.606 AC: 92134 AN: 151978 Hom.: 32707 Cov.: 31 AF XY: 0.613 AC XY: 45540 AN XY: 74264

African (AFR) AF: 0.209 AC: 8662 AN: 41446

American (AMR) AF: 0.763 AC: 11639 AN: 15256

Ashkenazi Jewish (ASJ) AF: 0.734 AC: 2548 AN: 3470

East Asian (EAS) AF: 0.916 AC: 4718 AN: 5152

South Asian (SAS) AF: 0.836 AC: 4037 AN: 4828

European-Finnish (FIN) AF: 0.706 AC: 7453 AN: 10564

Middle Eastern (MID) AF: 0.667 AC: 196 AN: 294

European-Non Finnish (NFE) AF: 0.747 AC: 50731 AN: 67952

Other (OTH) AF: 0.665 AC: 1400 AN: 2104

Alfa AF: 0.718 Hom.: 22174

Bravo AF: 0.593

Asia WGS AF: 0.854 AC: 2968 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	6.3
DANN	Benign	0.79
PhyloP100		0.48

Splicing

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

Other links and lift over

dbSNP: rs1405467; hg19: chr12-67556119;