12-23061041-C-T

Variant names:

• chr12-23061041-C-T
• rs12580249
• ENST00000538317.6:n.1271+3144C>T

Variant summary

Our verdict is Benign. The variant received -10 ACMG points: 0P and 10B. BP4_Moderate BA1

The ENST00000538317.6(LINC02955):​n.1271+3144C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0777 in 151,926 control chromosomes in the GnomAD database, including 640 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 0.078 (640 hom., cov: 32)
• Consequence: LINC02955 ENST00000538317.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.249
• Publications: 0 publications found

Genes affected

LINC02955 (HGNC:55973): (long intergenic non-protein coding RNA 2955)

ENSG00000309682 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -10 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.43).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.201 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000538317.6. 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
	LINC02955	NR_187500.1		n.1698+3144C>T		intron	N/A
	LINC02955	NR_187501.1		n.1373+3144C>T		intron	N/A
	LINC02955	NR_187503.1		n.1672+3144C>T		intron	N/A

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC02955	ENST00000538317.6	TSL:4	n.1271+3144C>T		intron	N/A
	LINC02955	ENST00000540895.6	TSL:2	n.1189+3144C>T		intron	N/A
	LINC02955	ENST00000625240.2	TSL:5	n.1084+3144C>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.0777 AC: 11788 AN: 151806 Hom.: 638 Cov.: 32

Gnomad AFR AF: 0.126

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0503

Gnomad ASJ AF: 0.0833

Gnomad EAS AF: 0.210

Gnomad SAS AF: 0.185

Gnomad FIN AF: 0.0823

Gnomad MID AF: 0.0481

Gnomad NFE AF: 0.0376

Gnomad OTH AF: 0.0503

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

GnomAD4 genome AF: 0.0777 AC: 11811 AN: 151926 Hom.: 640 Cov.: 32 AF XY: 0.0818 AC XY: 6069 AN XY: 74232

African (AFR) AF: 0.126 AC: 5233 AN: 41446

American (AMR) AF: 0.0507 AC: 772 AN: 15222

Ashkenazi Jewish (ASJ) AF: 0.0833 AC: 289 AN: 3470

East Asian (EAS) AF: 0.211 AC: 1087 AN: 5146

South Asian (SAS) AF: 0.183 AC: 880 AN: 4798

European-Finnish (FIN) AF: 0.0823 AC: 869 AN: 10554

Middle Eastern (MID) AF: 0.0445 AC: 13 AN: 292

European-Non Finnish (NFE) AF: 0.0376 AC: 2556 AN: 67976

Other (OTH) AF: 0.0531 AC: 112 AN: 2110

Alfa AF: 0.0514 Hom.: 106

Bravo AF: 0.0759

Asia WGS AF: 0.191 AC: 661 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.43
CADD	Benign	14
DANN	Benign	0.59
PhyloP100		0.25

Splicing

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

Other links and lift over

dbSNP: rs12580249; hg19: chr12-23213975;