rs683716

Variant names:

• chr12-113671349-G-A
• rs683716
• ENST00000661760.1:n.312+35522C>T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000661760.1(LINC01234):​n.312+35522C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.524 in 152,032 control chromosomes in the GnomAD database, including 21,872 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 0.52 (21872 hom., cov: 32)
• Consequence: LINC01234 ENST00000661760.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0900

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=-1.01).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.679 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.312+35522C>T		intron_variant	Intron 3 of 3

Frequencies

GnomAD3 genomes AF: 0.524 AC: 79533 AN: 151914 Hom.: 21835 Cov.: 32

Gnomad AFR AF: 0.685

Gnomad AMI AF: 0.342

Gnomad AMR AF: 0.526

Gnomad ASJ AF: 0.388

Gnomad EAS AF: 0.547

Gnomad SAS AF: 0.606

Gnomad FIN AF: 0.455

Gnomad MID AF: 0.434

Gnomad NFE AF: 0.438

Gnomad OTH AF: 0.500

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

GnomAD4 genome AF: 0.524 AC: 79628 AN: 152032 Hom.: 21872 Cov.: 32 AF XY: 0.526 AC XY: 39096 AN XY: 74300

Gnomad4 AFR AF: 0.685

Gnomad4 AMR AF: 0.526

Gnomad4 ASJ AF: 0.388

Gnomad4 EAS AF: 0.547

Gnomad4 SAS AF: 0.607

Gnomad4 FIN AF: 0.455

Gnomad4 NFE AF: 0.438

Gnomad4 OTH AF: 0.501

Alfa AF: 0.490 Hom.: 2437

Bravo AF: 0.531

Asia WGS AF: 0.580 AC: 2020 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	3.0
DANN	Benign	0.51

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs683716; hg19: chr12-114109154;