rs683716

Variant names:

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

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 2 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=-1.01).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.679 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.312+35522C>T		intron	N/A
	LINC01234	ENST00000762236.1		n.313-13618C>T		intron	N/A

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

African (AFR) AF: 0.685 AC: 28403 AN: 41438

American (AMR) AF: 0.526 AC: 8035 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.388 AC: 1348 AN: 3470

East Asian (EAS) AF: 0.547 AC: 2831 AN: 5172

South Asian (SAS) AF: 0.607 AC: 2922 AN: 4814

European-Finnish (FIN) AF: 0.455 AC: 4799 AN: 10550

Middle Eastern (MID) AF: 0.442 AC: 130 AN: 294

European-Non Finnish (NFE) AF: 0.438 AC: 29788 AN: 67990

Other (OTH) AF: 0.501 AC: 1060 AN: 2114

Alfa AF: 0.550 Hom.: 8949

Bravo AF: 0.531

Asia WGS AF: 0.580 AC: 2020 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	3.0
DANN	Benign	0.51
PhyloP100		-0.090

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs683716;

hg19: chr12-114109154;