rs7979865

Positions:

• chr12-22715231-C-T

Variant summary

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

The ENST00000536744.5(LINC02955):​n.154+15137C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.271 in 151,934 control chromosomes in the GnomAD database, including 5,919 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 0.27 (5919 hom., cov: 32)
• Consequence: LINC02955 ENST00000536744.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.233

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=-0.86).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.369 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LINC02955	NR_187497.1	n.321+6491C>T		intron_variant
LINC02955	NR_187498.1	n.236+15137C>T		intron_variant
LINC02955	NR_187499.1	n.321+6491C>T		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
LINC02955	ENST00000413794.6	n.236+15137C>T		intron_variant		4
LINC02955	ENST00000536744.5	n.154+15137C>T		intron_variant		2
LINC02955	ENST00000628326.1	n.68-8711C>T		intron_variant		5
LINC02955	ENST00000629824.2	n.226+6491C>T		intron_variant		5

Frequencies

GnomAD3 genomes AF: 0.271 AC: 41152 AN: 151818 Hom.: 5917 Cov.: 32

Gnomad AFR AF: 0.276

Gnomad AMI AF: 0.338

Gnomad AMR AF: 0.195

Gnomad ASJ AF: 0.363

Gnomad EAS AF: 0.0896

Gnomad SAS AF: 0.384

Gnomad FIN AF: 0.280

Gnomad MID AF: 0.361

Gnomad NFE AF: 0.283

Gnomad OTH AF: 0.275

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

GnomAD4 genome AF: 0.271 AC: 41168 AN: 151934 Hom.: 5919 Cov.: 32 AF XY: 0.270 AC XY: 20040 AN XY: 74270

Gnomad4 AFR AF: 0.276

Gnomad4 AMR AF: 0.195

Gnomad4 ASJ AF: 0.363

Gnomad4 EAS AF: 0.0898

Gnomad4 SAS AF: 0.384

Gnomad4 FIN AF: 0.280

Gnomad4 NFE AF: 0.283

Gnomad4 OTH AF: 0.273

Alfa AF: 0.284 Hom.: 3696

Bravo AF: 0.260

Asia WGS AF: 0.257 AC: 891 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	7.1
DANN	Benign	0.71

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7979865; hg19: chr12-22868165;