rs12872043

Variant names:

• chr13-55114111-G-A
• rs12872043
• ENST00000616578.2:n.288+7275G>A

Variant summary

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

The ENST00000616578.2(LINC02335):​n.288+7275G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.269 in 151,984 control chromosomes in the GnomAD database, including 5,750 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 0.27 (5750 hom., cov: 32)
• Consequence: LINC02335 ENST00000616578.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.421
• Publications: 1 publications found

Genes affected

LINC02335 (HGNC:53255): (long intergenic non-protein coding RNA 2335)

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.421 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000616578.2. 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
	LINC02335	NR_186625.1		n.850+7275G>A		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC02335	ENST00000616578.2	TSL:3	n.288+7275G>A		intron	N/A
	LINC02335	ENST00000732192.1		n.287+7275G>A		intron	N/A
	LINC02335	ENST00000732193.1		n.318-46846G>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.269 AC: 40806 AN: 151866 Hom.: 5746 Cov.: 32

Gnomad AFR AF: 0.205

Gnomad AMI AF: 0.489

Gnomad AMR AF: 0.259

Gnomad ASJ AF: 0.323

Gnomad EAS AF: 0.436

Gnomad SAS AF: 0.349

Gnomad FIN AF: 0.278

Gnomad MID AF: 0.370

Gnomad NFE AF: 0.283

Gnomad OTH AF: 0.292

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

GnomAD4 genome AF: 0.269 AC: 40815 AN: 151984 Hom.: 5750 Cov.: 32 AF XY: 0.272 AC XY: 20182 AN XY: 74288

African (AFR) AF: 0.204 AC: 8470 AN: 41442

American (AMR) AF: 0.259 AC: 3955 AN: 15264

Ashkenazi Jewish (ASJ) AF: 0.323 AC: 1119 AN: 3466

East Asian (EAS) AF: 0.436 AC: 2244 AN: 5152

South Asian (SAS) AF: 0.348 AC: 1677 AN: 4824

European-Finnish (FIN) AF: 0.278 AC: 2934 AN: 10572

Middle Eastern (MID) AF: 0.388 AC: 114 AN: 294

European-Non Finnish (NFE) AF: 0.283 AC: 19234 AN: 67948

Other (OTH) AF: 0.295 AC: 622 AN: 2110

Alfa AF: 0.282 Hom.: 3255

Bravo AF: 0.266

Asia WGS AF: 0.382 AC: 1325 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	0.65
DANN	Benign	0.56
PhyloP100		-0.42

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: rs12872043;

hg19: chr13-55688246;