rs7165988

chr15-38696614-C-Gchr15-38696614-C-T

Variant summary

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

The NR_160786.1(LINC02694):n.17C>G variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.289 in 1,611,242 control chromosomes in the GnomAD database, including 69,331 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 0.26 (5342 hom., cov: 32)
  • Exomes 𝑓: 0.29 (63989 hom.)
• Consequence: LINC02694 NR_160786.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.656

Genes affected

LINC02694 (HGNC:33796): (long intergenic non-protein coding RNA 2694)

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (MetaRNN=0.005088091).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.3 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LINC02694	NR_160786.1	n.17C>G		non_coding_transcript_exon_variant	1/2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
LINC02694	ENST00000644461.1	n.96+68459C>G		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.257 AC: 39063 AN: 152010 Hom.: 5342 Cov.: 32

Gnomad AFR AF: 0.196

Gnomad AMI AF: 0.269

Gnomad AMR AF: 0.269

Gnomad ASJ AF: 0.316

Gnomad EAS AF: 0.0939

Gnomad SAS AF: 0.207

Gnomad FIN AF: 0.258

Gnomad MID AF: 0.316

Gnomad NFE AF: 0.303

Gnomad OTH AF: 0.281

GnomAD3 exomes AF: 0.264 AC: 66097 AN: 250414 Hom.: 9325 AF XY: 0.266 AC XY: 36022 AN XY: 135328

Gnomad AFR exome AF: 0.192

Gnomad AMR exome AF: 0.261

Gnomad ASJ exome AF: 0.317

Gnomad EAS exome AF: 0.0937

Gnomad SAS exome AF: 0.221

Gnomad FIN exome AF: 0.262

Gnomad NFE exome AF: 0.309

Gnomad OTH exome AF: 0.292

GnomAD4 exome AF: 0.292 AC: 425924 AN: 1459114 Hom.: 63989 Cov.: 33 AF XY: 0.291 AC XY: 211332 AN XY: 725970

Gnomad4 AFR exome AF: 0.203

Gnomad4 AMR exome AF: 0.265

Gnomad4 ASJ exome AF: 0.312

Gnomad4 EAS exome AF: 0.0968

Gnomad4 SAS exome AF: 0.224

Gnomad4 FIN exome AF: 0.257

Gnomad4 NFE exome AF: 0.309

Gnomad4 OTH exome AF: 0.283

GnomAD4 genome AF: 0.257 AC: 39086 AN: 152128 Hom.: 5342 Cov.: 32 AF XY: 0.255 AC XY: 18950 AN XY: 74368

Gnomad4 AFR AF: 0.196

Gnomad4 AMR AF: 0.269

Gnomad4 ASJ AF: 0.316

Gnomad4 EAS AF: 0.0943

Gnomad4 SAS AF: 0.206

Gnomad4 FIN AF: 0.258

Gnomad4 NFE AF: 0.303

Gnomad4 OTH AF: 0.278

Alfa AF: 0.283 Hom.: 4821

Bravo AF: 0.261

TwinsUK AF: 0.316 AC: 1172

ALSPAC AF: 0.313 AC: 1207

ESP6500AA AF: 0.208 AC: 917

ESP6500EA AF: 0.303 AC: 2604

ExAC AF: 0.263 AC: 31869

Asia WGS AF: 0.152 AC: 526 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_addAF	Benign	-0.79	T
BayesDel_noAF	Benign	-0.76
Cadd	Benign	0.77
Dann	Benign	0.87
DEOGEN2	Benign	0.064	T
Eigen	Benign	-0.84
Eigen_PC	Benign	-1.0
FATHMM_MKL	Benign	0.035	N
LIST_S2	Benign	0.35	T
MetaRNN	Benign	0.0051	T
MetaSVM	Benign	-1.0	T
MutationAssessor	Benign	0.0	N
MutationTaster	Benign	1.0	P
PROVEAN	Benign	-2.0	N
REVEL	Benign	0.10
Sift4G	Pathogenic	0.0	D
Polyphen		0.97	D
Vest4		0.027
MPC		0.059
ClinPred		0.014	T
GERP RS		-0.56
Varity_R		0.29
gMVP		0.0075

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.020		Details are displayed if max score is > 0.2

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

Publications

LitVar

Other links and lift over

dbSNP: rs7165988; hg19: chr15-38988815; COSMIC: COSV59558592;