rs2046383

Variant names:

• chr12-29951209-T-G
• rs2046383
• XR_001749060.1:n.314-8169A>C

Variant summary

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

The XR_931474.1(LOC105369715):​n.314-8169A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.285 in 152,054 control chromosomes in the GnomAD database, including 6,235 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 0.29 (6235 hom., cov: 32)
• Consequence: LOC105369715 XR_931474.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.801
• Publications: 16 publications found

Genes affected

LOC105369715 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.358 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: 0.285 AC: 43277 AN: 151936 Hom.: 6219 Cov.: 32

Gnomad AFR AF: 0.293

Gnomad AMI AF: 0.322

Gnomad AMR AF: 0.233

Gnomad ASJ AF: 0.300

Gnomad EAS AF: 0.342

Gnomad SAS AF: 0.373

Gnomad FIN AF: 0.257

Gnomad MID AF: 0.392

Gnomad NFE AF: 0.283

Gnomad OTH AF: 0.317

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

GnomAD4 genome AF: 0.285 AC: 43343 AN: 152054 Hom.: 6235 Cov.: 32 AF XY: 0.285 AC XY: 21201 AN XY: 74344

African (AFR) AF: 0.294 AC: 12166 AN: 41448

American (AMR) AF: 0.232 AC: 3553 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.300 AC: 1042 AN: 3468

East Asian (EAS) AF: 0.342 AC: 1765 AN: 5162

South Asian (SAS) AF: 0.373 AC: 1797 AN: 4820

European-Finnish (FIN) AF: 0.257 AC: 2724 AN: 10600

Middle Eastern (MID) AF: 0.388 AC: 114 AN: 294

European-Non Finnish (NFE) AF: 0.283 AC: 19226 AN: 67956

Other (OTH) AF: 0.314 AC: 663 AN: 2114

Alfa AF: 0.290 Hom.: 29407

Bravo AF: 0.283

Asia WGS AF: 0.335 AC: 1166 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	0.11
DANN	Benign	0.83
PhyloP100		-0.80

Splicing

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

Other links and lift over

dbSNP: rs2046383; hg19: chr12-30104142;