rs763853

chr12-23169937-A-G

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_Moderate BA1

The ENST00000538317.6(LINC02955):n.1311+2859A>G variant causes a intron, non coding transcript 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, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 3.68

Genes affected

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

ACMG classification

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
LINC02955	ENST00000538317.6	n.1311+2859A>G		intron_variant, non_coding_transcript_variant		4

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

Gnomad4 AFR AF: 0.0698

Gnomad4 AMR AF: 0.0923

Gnomad4 ASJ AF: 0.178

Gnomad4 EAS AF: 0.188

Gnomad4 SAS AF: 0.184

Gnomad4 FIN AF: 0.150

Gnomad4 NFE AF: 0.107

Gnomad4 OTH AF: 0.104

Alfa AF: 0.110 Hom.: 2115

Bravo AF: 0.0981

Asia WGS AF: 0.192 AC: 665 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.39
Cadd	Benign	21
Dann	Benign	0.76

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs763853; hg19: chr12-23322871;