chr12-121132209-C-T

Variant names:

• chr12-121132209-C-T
• rs2393799
• XR_001749352.3:n.328-5368G>A

Variant summary

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

The XR_001749352.3(LOC105370032):​n.328-5368G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.386 in 152,006 control chromosomes in the GnomAD database, including 14,540 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 0.39 (14540 hom., cov: 31)
• Consequence: LOC105370032 XR_001749352.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.393
• Publications: 27 publications found

Genes affected

LOC105370032 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.698 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: 0.386 AC: 58587 AN: 151888 Hom.: 14485 Cov.: 31

Gnomad AFR AF: 0.704

Gnomad AMI AF: 0.190

Gnomad AMR AF: 0.224

Gnomad ASJ AF: 0.201

Gnomad EAS AF: 0.382

Gnomad SAS AF: 0.376

Gnomad FIN AF: 0.346

Gnomad MID AF: 0.180

Gnomad NFE AF: 0.251

Gnomad OTH AF: 0.323

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

GnomAD4 genome AF: 0.386 AC: 58714 AN: 152006 Hom.: 14540 Cov.: 31 AF XY: 0.384 AC XY: 28545 AN XY: 74280

African (AFR) AF: 0.704 AC: 29179 AN: 41428

American (AMR) AF: 0.224 AC: 3424 AN: 15268

Ashkenazi Jewish (ASJ) AF: 0.201 AC: 697 AN: 3470

East Asian (EAS) AF: 0.382 AC: 1971 AN: 5164

South Asian (SAS) AF: 0.378 AC: 1825 AN: 4824

European-Finnish (FIN) AF: 0.346 AC: 3657 AN: 10566

Middle Eastern (MID) AF: 0.197 AC: 58 AN: 294

European-Non Finnish (NFE) AF: 0.251 AC: 17044 AN: 67968

Other (OTH) AF: 0.325 AC: 686 AN: 2112

Alfa AF: 0.259 Hom.: 1293

Bravo AF: 0.386

Asia WGS AF: 0.405 AC: 1407 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	0.99
DANN	Benign	0.72
PhyloP100		-0.39

Splicing

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

Other links and lift over

dbSNP: rs2393799; hg19: chr12-121570012;