12-113604401-A-G

Variant names:

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

Variant summary

Our verdict is Benign. Variant got -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

Genes affected

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

ACMG classification

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC01234	ENST00000661760.1	n.313-18769T>C		intron_variant	Intron 3 of 3

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

Gnomad4 AFR AF: 0.462

Gnomad4 AMR AF: 0.326

Gnomad4 ASJ AF: 0.366

Gnomad4 EAS AF: 0.361

Gnomad4 SAS AF: 0.319

Gnomad4 FIN AF: 0.348

Gnomad4 NFE AF: 0.284

Gnomad4 OTH AF: 0.334

Alfa AF: 0.318 Hom.: 1699

Bravo AF: 0.354

Asia WGS AF: 0.347 AC: 1209 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4766691; hg19: chr12-114042206;