chr12-76009925-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.

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: 0.866 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 v4.9

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;