chr12-28080433-A-G

Variant names:

• chr12-28080433-A-G
• rs10492361
• XR_931462.3:n.8578T>C

Variant summary

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

The XR_931462.3(LOC105369710):​n.8578T>C variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.155 in 152,116 control chromosomes in the GnomAD database, including 2,449 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 0.16 (2449 hom., cov: 32)
• Consequence: LOC105369710 XR_931462.3 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.596
• Publications: 2 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=-0.91).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.233 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: 0.155 AC: 23589 AN: 151998 Hom.: 2450 Cov.: 32

Gnomad AFR AF: 0.0423

Gnomad AMI AF: 0.0954

Gnomad AMR AF: 0.131

Gnomad ASJ AF: 0.192

Gnomad EAS AF: 0.00386

Gnomad SAS AF: 0.0755

Gnomad FIN AF: 0.215

Gnomad MID AF: 0.152

Gnomad NFE AF: 0.236

Gnomad OTH AF: 0.177

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

GnomAD4 genome AF: 0.155 AC: 23583 AN: 152116 Hom.: 2449 Cov.: 32 AF XY: 0.150 AC XY: 11169 AN XY: 74318

African (AFR) AF: 0.0421 AC: 1748 AN: 41520

American (AMR) AF: 0.130 AC: 1992 AN: 15266

Ashkenazi Jewish (ASJ) AF: 0.192 AC: 666 AN: 3472

East Asian (EAS) AF: 0.00387 AC: 20 AN: 5172

South Asian (SAS) AF: 0.0762 AC: 367 AN: 4816

European-Finnish (FIN) AF: 0.215 AC: 2266 AN: 10564

Middle Eastern (MID) AF: 0.156 AC: 46 AN: 294

European-Non Finnish (NFE) AF: 0.236 AC: 16020 AN: 67992

Other (OTH) AF: 0.176 AC: 371 AN: 2108

Alfa AF: 0.213 Hom.: 6455

Bravo AF: 0.147

Asia WGS AF: 0.0420 AC: 150 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	1.5
DANN	Benign	0.41
PhyloP100		0.60

Splicing

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

Other links and lift over

dbSNP: rs10492361; hg19: chr12-28233366;