rs683716

Positions:

• chr12-113671349-G-A

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, non coding transcript 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, non_coding_transcript
• 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/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
LINC01234	ENST00000661760.1	n.312+35522C>T		intron_variant, non_coding_transcript_variant

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;