chr2-234302083-G-A

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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105373933	XR_007088124.1	n.-209C>T		upstream_gene_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt

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 v4.3

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;