12-16132784-C-T

Variant names:

• chr12-16132784-C-T
• rs1799465
• XR_001749028.1:n.62+25214C>T

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The XR_001749028.1(LOC101928362):​n.62+25214C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.858 in 152,222 control chromosomes in the GnomAD database, including 56,201 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 0.86 (56201 hom., cov: 32)
• Consequence: LOC101928362 XR_001749028.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.31
• Publications: 3 publications found

Genes affected

LOC101928362 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.87 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

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

Ensembl Transcripts

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

Frequencies

GnomAD3 genomes AF: 0.858 AC: 130570 AN: 152104 Hom.: 56168 Cov.: 32

Gnomad AFR AF: 0.865

Gnomad AMI AF: 0.966

Gnomad AMR AF: 0.850

Gnomad ASJ AF: 0.871

Gnomad EAS AF: 0.797

Gnomad SAS AF: 0.768

Gnomad FIN AF: 0.792

Gnomad MID AF: 0.831

Gnomad NFE AF: 0.876

Gnomad OTH AF: 0.846

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

GnomAD4 genome AF: 0.858 AC: 130655 AN: 152222 Hom.: 56201 Cov.: 32 AF XY: 0.852 AC XY: 63429 AN XY: 74418

African (AFR) AF: 0.865 AC: 35934 AN: 41536

American (AMR) AF: 0.850 AC: 12998 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.871 AC: 3021 AN: 3468

East Asian (EAS) AF: 0.796 AC: 4121 AN: 5176

South Asian (SAS) AF: 0.768 AC: 3704 AN: 4822

European-Finnish (FIN) AF: 0.792 AC: 8378 AN: 10584

Middle Eastern (MID) AF: 0.842 AC: 246 AN: 292

European-Non Finnish (NFE) AF: 0.876 AC: 59589 AN: 68022

Other (OTH) AF: 0.843 AC: 1783 AN: 2116

Alfa AF: 0.870 Hom.: 177532

Bravo AF: 0.864

Asia WGS AF: 0.751 AC: 2612 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.36
DANN	Benign	0.35
PhyloP100		-1.3

Splicing

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

Other links and lift over

dbSNP: rs1799465; hg19: chr12-16285718;