12-116347582-T-G

Variant names:

• chr12-116347582-T-G
• rs952417
• XR_945392.2:n.82-1332A>C

Variant summary

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

The XR_945392.2(LOC105370005):​n.82-1332A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.145 in 152,244 control chromosomes in the GnomAD database, including 1,958 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 0.14 (1958 hom., cov: 33)
• Consequence: LOC105370005 XR_945392.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.419
• Publications: 4 publications found

Genes affected

LOC105370005 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.82).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.315 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: 0.145 AC: 22059 AN: 152126 Hom.: 1959 Cov.: 33

Gnomad AFR AF: 0.0528

Gnomad AMI AF: 0.127

Gnomad AMR AF: 0.196

Gnomad ASJ AF: 0.125

Gnomad EAS AF: 0.328

Gnomad SAS AF: 0.116

Gnomad FIN AF: 0.190

Gnomad MID AF: 0.241

Gnomad NFE AF: 0.171

Gnomad OTH AF: 0.168

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

GnomAD4 genome AF: 0.145 AC: 22059 AN: 152244 Hom.: 1958 Cov.: 33 AF XY: 0.147 AC XY: 10953 AN XY: 74432

African (AFR) AF: 0.0526 AC: 2188 AN: 41560

American (AMR) AF: 0.196 AC: 2998 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.125 AC: 435 AN: 3470

East Asian (EAS) AF: 0.328 AC: 1702 AN: 5190

South Asian (SAS) AF: 0.117 AC: 565 AN: 4830

European-Finnish (FIN) AF: 0.190 AC: 2008 AN: 10590

Middle Eastern (MID) AF: 0.245 AC: 72 AN: 294

European-Non Finnish (NFE) AF: 0.171 AC: 11623 AN: 68012

Other (OTH) AF: 0.167 AC: 353 AN: 2116

Alfa AF: 0.152 Hom.: 1396

Bravo AF: 0.146

Asia WGS AF: 0.196 AC: 682 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	4.6
DANN	Benign	0.72
PhyloP100		0.42

Splicing

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

Other links and lift over

dbSNP: rs952417; hg19: chr12-116785387;