chr12-111369695-G-A

Variant names:

• chr12-111369695-G-A
• rs933399
• ENST00000548846.2:n.268+375G>A

Variant summary

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

The ENST00000548846.2(LINC02356):​n.268+375G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.421 in 151,920 control chromosomes in the GnomAD database, including 17,642 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 0.42 (17642 hom., cov: 31)
• Consequence: LINC02356 ENST00000548846.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.380
• Publications: 18 publications found

Genes affected

LINC02356 (HGNC:53278): (long intergenic non-protein coding RNA 2356)

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.908 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000548846.2. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC02356	NR_187520.1		n.60+375G>A		intron	N/A
	LINC02356	NR_187521.1		n.60+375G>A		intron	N/A
	LINC02356	NR_187522.1		n.60+375G>A		intron	N/A

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC02356	ENST00000548846.2	TSL:3	n.268+375G>A		intron	N/A
	LINC02356	ENST00000552663.3	TSL:3	n.258+375G>A		intron	N/A
	LINC02356	ENST00000722283.1		n.136+375G>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.421 AC: 63869 AN: 151804 Hom.: 17600 Cov.: 31

Gnomad AFR AF: 0.714

Gnomad AMI AF: 0.203

Gnomad AMR AF: 0.449

Gnomad ASJ AF: 0.146

Gnomad EAS AF: 0.931

Gnomad SAS AF: 0.580

Gnomad FIN AF: 0.231

Gnomad MID AF: 0.307

Gnomad NFE AF: 0.233

Gnomad OTH AF: 0.402

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

GnomAD4 genome AF: 0.421 AC: 63979 AN: 151920 Hom.: 17642 Cov.: 31 AF XY: 0.427 AC XY: 31662 AN XY: 74230

African (AFR) AF: 0.715 AC: 29581 AN: 41392

American (AMR) AF: 0.450 AC: 6874 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.146 AC: 505 AN: 3468

East Asian (EAS) AF: 0.930 AC: 4810 AN: 5170

South Asian (SAS) AF: 0.579 AC: 2782 AN: 4802

European-Finnish (FIN) AF: 0.231 AC: 2442 AN: 10564

Middle Eastern (MID) AF: 0.316 AC: 93 AN: 294

European-Non Finnish (NFE) AF: 0.233 AC: 15864 AN: 67948

Other (OTH) AF: 0.401 AC: 844 AN: 2106

Alfa AF: 0.298 Hom.: 10294

Bravo AF: 0.452

Asia WGS AF: 0.691 AC: 2399 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	7.1
DANN	Benign	0.89
PhyloP100		0.38

Splicing

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

Other links and lift over

dbSNP: rs933399; hg19: chr12-111807499;