12-28067783-T-G

Variant names:

• chr12-28067783-T-G
• rs708188
• XR_931461.3:n.156-3896A>C

Variant summary

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

The XR_931461.3(LOC105369710):​n.156-3896A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.749 in 151,932 control chromosomes in the GnomAD database, including 42,851 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 0.75 (42851 hom., cov: 30)
• Consequence: LOC105369710 XR_931461.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.05
• Publications: 6 publications found

Genes affected

LOC105369710 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.783 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: 0.749 AC: 113753 AN: 151814 Hom.: 42821 Cov.: 30

Gnomad AFR AF: 0.790

Gnomad AMI AF: 0.703

Gnomad AMR AF: 0.681

Gnomad ASJ AF: 0.719

Gnomad EAS AF: 0.724

Gnomad SAS AF: 0.702

Gnomad FIN AF: 0.786

Gnomad MID AF: 0.741

Gnomad NFE AF: 0.742

Gnomad OTH AF: 0.740

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

GnomAD4 genome AF: 0.749 AC: 113832 AN: 151932 Hom.: 42851 Cov.: 30 AF XY: 0.749 AC XY: 55621 AN XY: 74242

African (AFR) AF: 0.791 AC: 32769 AN: 41452

American (AMR) AF: 0.680 AC: 10368 AN: 15250

Ashkenazi Jewish (ASJ) AF: 0.719 AC: 2491 AN: 3466

East Asian (EAS) AF: 0.724 AC: 3725 AN: 5148

South Asian (SAS) AF: 0.700 AC: 3372 AN: 4814

European-Finnish (FIN) AF: 0.786 AC: 8285 AN: 10544

Middle Eastern (MID) AF: 0.731 AC: 215 AN: 294

European-Non Finnish (NFE) AF: 0.742 AC: 50409 AN: 67952

Other (OTH) AF: 0.741 AC: 1561 AN: 2106

Alfa AF: 0.743 Hom.: 121253

Bravo AF: 0.747

Asia WGS AF: 0.745 AC: 2593 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.64
DANN	Benign	0.53
PhyloP100		-1.1

Splicing

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

Other links and lift over

dbSNP: rs708188; hg19: chr12-28220716;