12-113604401-A-G

Variant names:

• chr12-113604401-A-G
• rs4766691
• ENST00000661760.1:n.313-18769T>C

Variant summary

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

The ENST00000661760.1(LINC01234):​n.313-18769T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.348 in 151,950 control chromosomes in the GnomAD database, including 9,561 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 0.35 (9561 hom., cov: 31)
• Consequence: LINC01234 ENST00000661760.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.691
• Publications: 4 publications found

Genes affected

LINC01234 (HGNC:49757): (long intergenic non-protein coding RNA 1234)

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.456 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000661760.1. You can select a different transcript below to see updated ACMG assignments.

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
	LINC01234	ENST00000661760.1		n.313-18769T>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.348 AC: 52775 AN: 151832 Hom.: 9557 Cov.: 31

Gnomad AFR AF: 0.462

Gnomad AMI AF: 0.293

Gnomad AMR AF: 0.326

Gnomad ASJ AF: 0.366

Gnomad EAS AF: 0.361

Gnomad SAS AF: 0.320

Gnomad FIN AF: 0.348

Gnomad MID AF: 0.320

Gnomad NFE AF: 0.284

Gnomad OTH AF: 0.332

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

GnomAD4 genome AF: 0.348 AC: 52831 AN: 151950 Hom.: 9561 Cov.: 31 AF XY: 0.345 AC XY: 25659 AN XY: 74270

African (AFR) AF: 0.462 AC: 19125 AN: 41422

American (AMR) AF: 0.326 AC: 4973 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.366 AC: 1270 AN: 3470

East Asian (EAS) AF: 0.361 AC: 1865 AN: 5160

South Asian (SAS) AF: 0.319 AC: 1536 AN: 4812

European-Finnish (FIN) AF: 0.348 AC: 3666 AN: 10548

Middle Eastern (MID) AF: 0.333 AC: 98 AN: 294

European-Non Finnish (NFE) AF: 0.284 AC: 19327 AN: 67958

Other (OTH) AF: 0.334 AC: 705 AN: 2108

Alfa AF: 0.321 Hom.: 3085

Bravo AF: 0.354

Asia WGS AF: 0.347 AC: 1209 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	0.63
DANN	Benign	0.37
PhyloP100		-0.69

Splicing

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

Other links and lift over

dbSNP: rs4766691; hg19: chr12-114042206;