12-131245772-T-G

Variant names:

• chr12-131245772-T-G
• rs4387437
• XR_945558.3:n.891-6870A>C

Variant summary

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

The XR_945558.3(LOC105370082):​n.891-6870A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.611 in 151,470 control chromosomes in the GnomAD database, including 28,795 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 (28795 hom., cov: 33)
• Consequence: LOC105370082 XR_945558.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.346
• Publications: 5 publications found

Genes affected

LOC105370082 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.23).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.689 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: 0.610 AC: 92392 AN: 151352 Hom.: 28732 Cov.: 33

Gnomad AFR AF: 0.695

Gnomad AMI AF: 0.628

Gnomad AMR AF: 0.659

Gnomad ASJ AF: 0.584

Gnomad EAS AF: 0.359

Gnomad SAS AF: 0.609

Gnomad FIN AF: 0.470

Gnomad MID AF: 0.657

Gnomad NFE AF: 0.590

Gnomad OTH AF: 0.612

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

GnomAD4 genome AF: 0.611 AC: 92516 AN: 151470 Hom.: 28795 Cov.: 33 AF XY: 0.607 AC XY: 44948 AN XY: 74030

African (AFR) AF: 0.696 AC: 28859 AN: 41482

American (AMR) AF: 0.659 AC: 10010 AN: 15190

Ashkenazi Jewish (ASJ) AF: 0.584 AC: 2017 AN: 3456

East Asian (EAS) AF: 0.360 AC: 1850 AN: 5140

South Asian (SAS) AF: 0.610 AC: 2942 AN: 4824

European-Finnish (FIN) AF: 0.470 AC: 4922 AN: 10472

Middle Eastern (MID) AF: 0.669 AC: 194 AN: 290

European-Non Finnish (NFE) AF: 0.590 AC: 39861 AN: 67608

Other (OTH) AF: 0.615 AC: 1291 AN: 2100

Alfa AF: 0.594 Hom.: 72594

Bravo AF: 0.625

Asia WGS AF: 0.504 AC: 1756 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.2
CADD	Benign	0.54
DANN	Benign	0.25
PhyloP100		-0.35

Splicing

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

Other links and lift over

dbSNP: rs4387437; hg19: chr12-131730317;