12-76009925-T-C

Variant names:

• chr12-76009925-T-C
• rs4831958
• XR_945110.4:n.-243A>G

Variant summary

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

The XR_945110.4(LOC105369847):​n.-243A>G variant causes a upstream gene change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.866 in 152,196 control chromosomes in the GnomAD database, including 57,972 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 0.87 (57972 hom., cov: 32)
• Consequence: LOC105369847 XR_945110.4 upstream_gene
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.437
• Publications: 1 publications found

Genes affected

LOC105369847 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.54).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.976 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105369847	XR_945110.4	n.-243A>G		upstream_gene_variant

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.866 AC: 131674 AN: 152078 Hom.: 57934 Cov.: 32

Gnomad AFR AF: 0.697

Gnomad AMI AF: 0.956

Gnomad AMR AF: 0.902

Gnomad ASJ AF: 0.860

Gnomad EAS AF: 0.999

Gnomad SAS AF: 0.926

Gnomad FIN AF: 0.976

Gnomad MID AF: 0.896

Gnomad NFE AF: 0.927

Gnomad OTH AF: 0.879

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

GnomAD4 genome AF: 0.866 AC: 131767 AN: 152196 Hom.: 57972 Cov.: 32 AF XY: 0.870 AC XY: 64766 AN XY: 74402

African (AFR) AF: 0.697 AC: 28926 AN: 41472

American (AMR) AF: 0.902 AC: 13787 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.860 AC: 2983 AN: 3470

East Asian (EAS) AF: 0.999 AC: 5172 AN: 5176

South Asian (SAS) AF: 0.927 AC: 4480 AN: 4834

European-Finnish (FIN) AF: 0.976 AC: 10358 AN: 10618

Middle Eastern (MID) AF: 0.901 AC: 265 AN: 294

European-Non Finnish (NFE) AF: 0.927 AC: 63062 AN: 68020

Other (OTH) AF: 0.882 AC: 1862 AN: 2112

Alfa AF: 0.906 Hom.: 102720

Bravo AF: 0.851

Asia WGS AF: 0.948 AC: 3294 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.54
CADD	Benign	9.6
DANN	Benign	0.74
PhyloP100		0.44

Splicing

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

Other links and lift over

dbSNP: rs4831958; hg19: chr12-76403705;