12-54196315-C-T

Variant names:

• chr12-54196315-C-T
• rs2029166
• XR_944983.1:n.367-4145C>T

Variant summary

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

The XR_944983.1(LOC105369777):​n.367-4145C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.334 in 151,962 control chromosomes in the GnomAD database, including 8,963 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 0.33 (8963 hom., cov: 31)
• Consequence: LOC105369777 XR_944983.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.37
• Publications: 19 publications found

Genes affected

LOC105369777 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.61).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.453 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: 0.334 AC: 50765 AN: 151844 Hom.: 8963 Cov.: 31

Gnomad AFR AF: 0.401

Gnomad AMI AF: 0.193

Gnomad AMR AF: 0.314

Gnomad ASJ AF: 0.307

Gnomad EAS AF: 0.441

Gnomad SAS AF: 0.470

Gnomad FIN AF: 0.409

Gnomad MID AF: 0.320

Gnomad NFE AF: 0.273

Gnomad OTH AF: 0.304

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

GnomAD4 genome AF: 0.334 AC: 50778 AN: 151962 Hom.: 8963 Cov.: 31 AF XY: 0.342 AC XY: 25426 AN XY: 74282

African (AFR) AF: 0.401 AC: 16605 AN: 41434

American (AMR) AF: 0.313 AC: 4782 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.307 AC: 1067 AN: 3472

East Asian (EAS) AF: 0.441 AC: 2266 AN: 5142

South Asian (SAS) AF: 0.469 AC: 2260 AN: 4820

European-Finnish (FIN) AF: 0.409 AC: 4310 AN: 10550

Middle Eastern (MID) AF: 0.327 AC: 96 AN: 294

European-Non Finnish (NFE) AF: 0.273 AC: 18584 AN: 67960

Other (OTH) AF: 0.300 AC: 632 AN: 2108

Alfa AF: 0.282 Hom.: 10413

Bravo AF: 0.327

Asia WGS AF: 0.429 AC: 1494 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.61
CADD	Benign	6.7
DANN	Benign	0.88
PhyloP100		-1.4

Splicing

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

Other links and lift over

dbSNP: rs2029166; hg19: chr12-54590099;