12-22717208-A-G

Variant names:

• chr12-22717208-A-G
• rs261926
• ENST00000413794.6:n.236+17114A>G

Variant summary

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

The ENST00000413794.6(LINC02955):​n.236+17114A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.411 in 151,894 control chromosomes in the GnomAD database, including 14,394 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 0.41 (14394 hom., cov: 33)
• Consequence: LINC02955 ENST00000413794.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.16
• Publications: 6 publications found

Genes affected

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

ENSG00000299158 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.517 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000413794.6. 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_187497.1		n.321+8468A>G		intron	N/A
	LINC02955	NR_187498.1		n.236+17114A>G		intron	N/A
	LINC02955	NR_187499.1		n.321+8468A>G		intron	N/A

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC02955	ENST00000413794.6	TSL:4	n.236+17114A>G		intron	N/A
	LINC02955	ENST00000536744.5	TSL:2	n.154+17114A>G		intron	N/A
	LINC02955	ENST00000628326.1	TSL:5	n.68-6734A>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.412 AC: 62460 AN: 151776 Hom.: 14390 Cov.: 33

Gnomad AFR AF: 0.254

Gnomad AMI AF: 0.423

Gnomad AMR AF: 0.496

Gnomad ASJ AF: 0.415

Gnomad EAS AF: 0.0873

Gnomad SAS AF: 0.208

Gnomad FIN AF: 0.449

Gnomad MID AF: 0.385

Gnomad NFE AF: 0.522

Gnomad OTH AF: 0.418

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

GnomAD4 genome AF: 0.411 AC: 62493 AN: 151894 Hom.: 14394 Cov.: 33 AF XY: 0.405 AC XY: 30037 AN XY: 74232

African (AFR) AF: 0.254 AC: 10499 AN: 41416

American (AMR) AF: 0.496 AC: 7579 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.415 AC: 1437 AN: 3466

East Asian (EAS) AF: 0.0877 AC: 454 AN: 5176

South Asian (SAS) AF: 0.209 AC: 1005 AN: 4820

European-Finnish (FIN) AF: 0.449 AC: 4727 AN: 10518

Middle Eastern (MID) AF: 0.390 AC: 114 AN: 292

European-Non Finnish (NFE) AF: 0.522 AC: 35418 AN: 67904

Other (OTH) AF: 0.414 AC: 876 AN: 2116

Alfa AF: 0.479 Hom.: 68822

Bravo AF: 0.411

Asia WGS AF: 0.162 AC: 565 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	7.9
DANN	Benign	0.91
PhyloP100		1.2

Splicing

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

Other links and lift over

dbSNP: rs261926; hg19: chr12-22870142;