12-22717208-A-G

Variant summary

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

The XR_001749045.2(LINC02955):n.321+8468A>G 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 0.411 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 XR_001749045.2 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.16

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=-0.85).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.517 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LINC02955	XR_001749045.2	n.321+8468A>G		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
LINC02955	ENST00000413794.6	n.236+17114A>G		intron_variant, non_coding_transcript_variant		4
LINC02955	ENST00000536744.5	n.154+17114A>G		intron_variant, non_coding_transcript_variant		2
LINC02955	ENST00000628326.1	n.68-6734A>G		intron_variant, non_coding_transcript_variant		5
LINC02955	ENST00000629824.2	n.226+8468A>G		intron_variant, non_coding_transcript_variant		5

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

Gnomad4 AFR AF: 0.254

Gnomad4 AMR AF: 0.496

Gnomad4 ASJ AF: 0.415

Gnomad4 EAS AF: 0.0877

Gnomad4 SAS AF: 0.209

Gnomad4 FIN AF: 0.449

Gnomad4 NFE AF: 0.522

Gnomad4 OTH AF: 0.414

Alfa AF: 0.490 Hom.: 29116

Bravo AF: 0.411

Asia WGS AF: 0.162 AC: 565 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
Cadd	Benign	7.9
Dann	Benign	0.91

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs261926; hg19: chr12-22870142;