12-23036062-G-C

Position:

• chr12-23036062-G-C

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000538317.6(LINC02955):​n.764-10046G>C variant causes a intron, non coding transcript 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, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.363

Genes affected

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

ACMG classification

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
LINC02955	ENST00000538317.6	n.764-10046G>C		intron_variant, non_coding_transcript_variant		4

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

Gnomad4 AFR AF: 0.175

Gnomad4 AMR AF: 0.553

Gnomad4 ASJ AF: 0.585

Gnomad4 EAS AF: 0.315

Gnomad4 SAS AF: 0.394

Gnomad4 FIN AF: 0.530

Gnomad4 NFE AF: 0.576

Gnomad4 OTH AF: 0.489

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 v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10842101; hg19: chr12-23188996;