rs833718

Variant names:

• chr12-102677308-G-A
• rs833718
• ENST00000737486.1:n.122-12798G>A

Variant summary

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

The ENST00000737486.1(ENSG00000296233):​n.122-12798G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.433 in 152,030 control chromosomes in the GnomAD database, including 14,535 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 0.43 (14535 hom., cov: 33)
• Consequence: ENSG00000296233 ENST00000737486.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.256
• Publications: 4 publications found

Genes affected

ENSG00000296233 (HGNC:):

LINC02456 (HGNC:53389): (long intergenic non-protein coding RNA 2456)

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.528 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000737486.1. 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
	ENSG00000296233	ENST00000737486.1		n.122-12798G>A		intron	N/A
	ENSG00000296233	ENST00000737487.1		n.122-12798G>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.433 AC: 65810 AN: 151912 Hom.: 14517 Cov.: 33

Gnomad AFR AF: 0.372

Gnomad AMI AF: 0.595

Gnomad AMR AF: 0.396

Gnomad ASJ AF: 0.508

Gnomad EAS AF: 0.545

Gnomad SAS AF: 0.505

Gnomad FIN AF: 0.396

Gnomad MID AF: 0.585

Gnomad NFE AF: 0.464

Gnomad OTH AF: 0.456

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

GnomAD4 genome AF: 0.433 AC: 65866 AN: 152030 Hom.: 14535 Cov.: 33 AF XY: 0.431 AC XY: 32043 AN XY: 74300

African (AFR) AF: 0.372 AC: 15420 AN: 41452

American (AMR) AF: 0.396 AC: 6055 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.508 AC: 1765 AN: 3472

East Asian (EAS) AF: 0.545 AC: 2820 AN: 5172

South Asian (SAS) AF: 0.506 AC: 2435 AN: 4814

European-Finnish (FIN) AF: 0.396 AC: 4187 AN: 10560

Middle Eastern (MID) AF: 0.575 AC: 169 AN: 294

European-Non Finnish (NFE) AF: 0.463 AC: 31500 AN: 67966

Other (OTH) AF: 0.462 AC: 974 AN: 2106

Alfa AF: 0.459 Hom.: 45017

Bravo AF: 0.433

Asia WGS AF: 0.527 AC: 1830 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	11
DANN	Benign	0.67
PhyloP100		-0.26

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: rs833718;

hg19: chr12-103071086;