12-23169937-A-G

Variant names:

• chr12-23169937-A-G
• rs763853
• ENST00000538317.6:n.1311+2859A>G

Variant summary

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

The ENST00000538317.6(LINC02955):​n.1311+2859A>G variant causes a intron change. The variant allele was found at a frequency of 0.105 in 152,200 control chromosomes in the GnomAD database, including 932 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 0.10 (932 hom., cov: 32)
• Consequence: LINC02955 ENST00000538317.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 3.68
• Publications: 6 publications found

Genes affected

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

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.39).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.179 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.1699-3452A>G		intron	N/A
	LINC02955	NR_187501.1		n.1413+2859A>G		intron	N/A
	LINC02955	NR_187503.1		n.1712+2859A>G		intron	N/A

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC02955	ENST00000538317.6	TSL:4	n.1311+2859A>G		intron	N/A
	LINC02955	ENST00000540895.6	TSL:2	n.1190-3452A>G		intron	N/A
	LINC02955	ENST00000541288.5	TSL:3	n.109-15537A>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.105 AC: 15922 AN: 152082 Hom.: 939 Cov.: 32

Gnomad AFR AF: 0.0697

Gnomad AMI AF: 0.0208

Gnomad AMR AF: 0.0918

Gnomad ASJ AF: 0.178

Gnomad EAS AF: 0.189

Gnomad SAS AF: 0.186

Gnomad FIN AF: 0.150

Gnomad MID AF: 0.133

Gnomad NFE AF: 0.107

Gnomad OTH AF: 0.104

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

GnomAD4 genome AF: 0.105 AC: 15931 AN: 152200 Hom.: 932 Cov.: 32 AF XY: 0.109 AC XY: 8108 AN XY: 74430

African (AFR) AF: 0.0698 AC: 2899 AN: 41558

American (AMR) AF: 0.0923 AC: 1410 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.178 AC: 618 AN: 3470

East Asian (EAS) AF: 0.188 AC: 971 AN: 5154

South Asian (SAS) AF: 0.184 AC: 889 AN: 4820

European-Finnish (FIN) AF: 0.150 AC: 1592 AN: 10606

Middle Eastern (MID) AF: 0.136 AC: 40 AN: 294

European-Non Finnish (NFE) AF: 0.107 AC: 7274 AN: 67994

Other (OTH) AF: 0.104 AC: 219 AN: 2114

Alfa AF: 0.108 Hom.: 4303

Bravo AF: 0.0981

Asia WGS AF: 0.192 AC: 665 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.39
CADD	Benign	21
DANN	Benign	0.76
PhyloP100		3.7

Splicing

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

Other links and lift over

dbSNP: rs763853; hg19: chr12-23322871;