12-23036062-G-C

Variant names:

• chr12-23036062-G-C
• rs10842101
• ENST00000538317.6:n.764-10046G>C

Variant summary

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

The ENST00000538317.6(LINC02955):​n.764-10046G>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.445 in 151,940 control chromosomes in the GnomAD database, including 17,398 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 0.45 (17398 hom., cov: 31)
• Consequence: LINC02955 ENST00000538317.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.363
• Publications: 0 publications found

Genes affected

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

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.572 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.1022-10046G>C		intron	N/A
	LINC02955	NR_187501.1		n.866-10046G>C		intron	N/A
	LINC02955	NR_187503.1		n.1090-17929G>C		intron	N/A

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC02955	ENST00000538317.6	TSL:4	n.764-10046G>C		intron	N/A
	LINC02955	ENST00000540895.6	TSL:2	n.513-10046G>C		intron	N/A
	LINC02955	ENST00000540994.1	TSL:3	n.115-2440G>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.445 AC: 67613 AN: 151822 Hom.: 17390 Cov.: 31

Gnomad AFR AF: 0.174

Gnomad AMI AF: 0.504

Gnomad AMR AF: 0.553

Gnomad ASJ AF: 0.585

Gnomad EAS AF: 0.315

Gnomad SAS AF: 0.393

Gnomad FIN AF: 0.530

Gnomad MID AF: 0.560

Gnomad NFE AF: 0.576

Gnomad OTH AF: 0.492

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

GnomAD4 genome AF: 0.445 AC: 67639 AN: 151940 Hom.: 17398 Cov.: 31 AF XY: 0.446 AC XY: 33070 AN XY: 74230

African (AFR) AF: 0.175 AC: 7232 AN: 41438

American (AMR) AF: 0.553 AC: 8446 AN: 15262

Ashkenazi Jewish (ASJ) AF: 0.585 AC: 2030 AN: 3472

East Asian (EAS) AF: 0.315 AC: 1620 AN: 5142

South Asian (SAS) AF: 0.394 AC: 1899 AN: 4814

European-Finnish (FIN) AF: 0.530 AC: 5583 AN: 10542

Middle Eastern (MID) AF: 0.558 AC: 164 AN: 294

European-Non Finnish (NFE) AF: 0.576 AC: 39171 AN: 67950

Other (OTH) AF: 0.489 AC: 1034 AN: 2114

Alfa AF: 0.355 Hom.: 1017

Bravo AF: 0.434

Asia WGS AF: 0.370 AC: 1290 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	1.0
DANN	Benign	0.28
PhyloP100		-0.36

Splicing

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

Other links and lift over

dbSNP: rs10842101; hg19: chr12-23188996;