chr12-12576382-G-A

Variant names:

• chr12-12576382-G-A
• rs12302103
• XR_001749010.1:n.659-44C>T

Variant summary

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

The XR_001749010.1(LOC107984486):​n.659-44C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.186 in 152,010 control chromosomes in the GnomAD database, including 3,252 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 0.19 (3252 hom., cov: 31)
• Consequence: LOC107984486 XR_001749010.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0770
• Publications: 4 publications found

Genes affected

LOC107984486 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.82).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.259 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: 0.186 AC: 28216 AN: 151894 Hom.: 3248 Cov.: 31

Gnomad AFR AF: 0.0746

Gnomad AMI AF: 0.173

Gnomad AMR AF: 0.232

Gnomad ASJ AF: 0.246

Gnomad EAS AF: 0.00618

Gnomad SAS AF: 0.120

Gnomad FIN AF: 0.156

Gnomad MID AF: 0.255

Gnomad NFE AF: 0.262

Gnomad OTH AF: 0.204

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

GnomAD4 genome AF: 0.186 AC: 28228 AN: 152010 Hom.: 3252 Cov.: 31 AF XY: 0.180 AC XY: 13381 AN XY: 74254

African (AFR) AF: 0.0744 AC: 3087 AN: 41482

American (AMR) AF: 0.232 AC: 3546 AN: 15260

Ashkenazi Jewish (ASJ) AF: 0.246 AC: 852 AN: 3464

East Asian (EAS) AF: 0.00600 AC: 31 AN: 5170

South Asian (SAS) AF: 0.120 AC: 578 AN: 4810

European-Finnish (FIN) AF: 0.156 AC: 1649 AN: 10538

Middle Eastern (MID) AF: 0.267 AC: 78 AN: 292

European-Non Finnish (NFE) AF: 0.262 AC: 17822 AN: 67976

Other (OTH) AF: 0.203 AC: 427 AN: 2106

Alfa AF: 0.218 Hom.: 2650

Bravo AF: 0.186

Asia WGS AF: 0.0700 AC: 247 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	1.6
DANN	Benign	0.30
PhyloP100		0.077

Splicing

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

Other links and lift over

dbSNP: rs12302103; hg19: chr12-12729316;