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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105369777	XR_944983.1	n.367-4145C>T		intron_variant	Intron 3 of 3
LOC105369777	XR_944984.2	n.194-4145C>T		intron_variant	Intron 2 of 2

Ensembl

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

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 v4.3

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;