rs12151790

Variant names:

• chr2-234302083-G-A
• rs12151790
• XR_007088124.1:n.-209C>T

Variant summary

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

The XR_007088124.1(LOC105373933):​n.-209C>T variant causes a upstream gene change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.131 in 152,104 control chromosomes in the GnomAD database, including 2,286 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 0.13 (2286 hom., cov: 32)
• Consequence: LOC105373933 XR_007088124.1 upstream_gene
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.539
• Publications: 9 publications found

Genes affected

LOC105373933 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.304 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: 0.130 AC: 19805 AN: 151986 Hom.: 2277 Cov.: 32

Gnomad AFR AF: 0.308

Gnomad AMI AF: 0.00877

Gnomad AMR AF: 0.0757

Gnomad ASJ AF: 0.0888

Gnomad EAS AF: 0.147

Gnomad SAS AF: 0.110

Gnomad FIN AF: 0.0772

Gnomad MID AF: 0.111

Gnomad NFE AF: 0.0465

Gnomad OTH AF: 0.141

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

GnomAD4 genome AF: 0.131 AC: 19855 AN: 152104 Hom.: 2286 Cov.: 32 AF XY: 0.130 AC XY: 9677 AN XY: 74370

African (AFR) AF: 0.308 AC: 12782 AN: 41436

American (AMR) AF: 0.0756 AC: 1156 AN: 15298

Ashkenazi Jewish (ASJ) AF: 0.0888 AC: 308 AN: 3468

East Asian (EAS) AF: 0.147 AC: 763 AN: 5176

South Asian (SAS) AF: 0.110 AC: 530 AN: 4822

European-Finnish (FIN) AF: 0.0772 AC: 817 AN: 10586

Middle Eastern (MID) AF: 0.0986 AC: 29 AN: 294

European-Non Finnish (NFE) AF: 0.0466 AC: 3166 AN: 67996

Other (OTH) AF: 0.140 AC: 296 AN: 2116

Alfa AF: 0.479 Hom.: 7082

Bravo AF: 0.137

Asia WGS AF: 0.150 AC: 521 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	2.4
DANN	Benign	0.23
PhyloP100		-0.54

Splicing

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

Other links and lift over

dbSNP: rs12151790; hg19: chr2-235210727;