rs210162

Positions:

• chr6-33593119-A-G
• chr6-33593119-A-T

Variant summary

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

The NR_027908.2(LINC00336):​n.220T>C 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 0.237 in 404,854 control chromosomes in the GnomAD database, including 13,344 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 0.22 (4047 hom., cov: 34)
  • Exomes 𝑓: 0.25 (9297 hom.)
• Consequence: LINC00336 NR_027908.2 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.206

Genes affected

LINC00336 (HGNC:33813): (long intergenic non-protein coding RNA 336)

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.48 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LINC00336	NR_027908.2	n.220T>C		non_coding_transcript_exon_variant	1/2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
LINC00336	ENST00000477984.1	n.220T>C		non_coding_transcript_exon_variant	1/2	2
LINC00336	ENST00000689377.1	n.198T>C		non_coding_transcript_exon_variant	1/2

Frequencies

GnomAD3 genomes AF: 0.217 AC: 33039 AN: 152062 Hom.: 4038 Cov.: 34

Gnomad AFR AF: 0.176

Gnomad AMI AF: 0.218

Gnomad AMR AF: 0.229

Gnomad ASJ AF: 0.212

Gnomad EAS AF: 0.497

Gnomad SAS AF: 0.406

Gnomad FIN AF: 0.158

Gnomad MID AF: 0.241

Gnomad NFE AF: 0.214

Gnomad OTH AF: 0.255

GnomAD3 exomes AF: 0.255 AC: 29084 AN: 114128 Hom.: 4595 AF XY: 0.268 AC XY: 15903 AN XY: 59232

Gnomad AFR exome AF: 0.171

Gnomad AMR exome AF: 0.186

Gnomad ASJ exome AF: 0.214

Gnomad EAS exome AF: 0.516

Gnomad SAS exome AF: 0.406

Gnomad FIN exome AF: 0.160

Gnomad NFE exome AF: 0.221

Gnomad OTH exome AF: 0.242

GnomAD4 exome AF: 0.250 AC: 63074 AN: 252674 Hom.: 9297 Cov.: 0 AF XY: 0.268 AC XY: 37210 AN XY: 138614

Gnomad4 AFR exome AF: 0.164

Gnomad4 AMR exome AF: 0.183

Gnomad4 ASJ exome AF: 0.211

Gnomad4 EAS exome AF: 0.506

Gnomad4 SAS exome AF: 0.386

Gnomad4 FIN exome AF: 0.158

Gnomad4 NFE exome AF: 0.214

Gnomad4 OTH exome AF: 0.238

GnomAD4 genome AF: 0.217 AC: 33057 AN: 152180 Hom.: 4047 Cov.: 34 AF XY: 0.220 AC XY: 16407 AN XY: 74412

Gnomad4 AFR AF: 0.175

Gnomad4 AMR AF: 0.229

Gnomad4 ASJ AF: 0.212

Gnomad4 EAS AF: 0.496

Gnomad4 SAS AF: 0.407

Gnomad4 FIN AF: 0.158

Gnomad4 NFE AF: 0.214

Gnomad4 OTH AF: 0.263

Alfa AF: 0.216 Hom.: 4559

Bravo AF: 0.217

Asia WGS AF: 0.476 AC: 1656 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	2.7
DANN	Benign	0.29

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs210162; hg19: chr6-33560896; COSMIC: COSV65668190;