rs7979865

Variant names:

• chr12-22715231-C-T
• rs7979865
• ENST00000413794.6:n.236+15137C>T

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000413794.6(LINC02955):​n.236+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 ENST00000413794.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.233
• Publications: 5 publications found

Genes affected

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

ENSG00000299158 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000413794.6. 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_187497.1		n.321+6491C>T		intron	N/A
	LINC02955	NR_187498.1		n.236+15137C>T		intron	N/A
	LINC02955	NR_187499.1		n.321+6491C>T		intron	N/A

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC02955	ENST00000413794.6	TSL:4	n.236+15137C>T		intron	N/A
	LINC02955	ENST00000536744.5	TSL:2	n.154+15137C>T		intron	N/A
	LINC02955	ENST00000628326.1	TSL:5	n.68-8711C>T		intron	N/A

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

African (AFR) AF: 0.276 AC: 11418 AN: 41350

American (AMR) AF: 0.195 AC: 2975 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.363 AC: 1258 AN: 3468

East Asian (EAS) AF: 0.0898 AC: 465 AN: 5176

South Asian (SAS) AF: 0.384 AC: 1850 AN: 4822

European-Finnish (FIN) AF: 0.280 AC: 2957 AN: 10564

Middle Eastern (MID) AF: 0.349 AC: 102 AN: 292

European-Non Finnish (NFE) AF: 0.283 AC: 19258 AN: 67960

Other (OTH) AF: 0.273 AC: 577 AN: 2116

Alfa AF: 0.284 Hom.: 4046

Bravo AF: 0.260

Asia WGS AF: 0.257 AC: 891 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	7.1
DANN	Benign	0.71
PhyloP100		0.23

Splicing

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

Other links and lift over

dbSNP: rs7979865; hg19: chr12-22868165;