rs210162

Variant names:

• chr6-33593119-A-G
• rs210162
• ENST00000477984.1:n.220T>C

Your query was ambiguous. Multiple possible variants found:

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

Variant summary

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

The ENST00000477984.1(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 ENST00000477984.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.206
• Publications: 17 publications found

Genes affected

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

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt
LINC00336	NR_027908.2	n.220T>C		non_coding_transcript_exon_variant	Exon 1 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC00336	ENST00000477984.1	n.220T>C		non_coding_transcript_exon_variant	Exon 1 of 2	2
LINC00336	ENST00000689377.2	n.220T>C		non_coding_transcript_exon_variant	Exon 1 of 2
LINC00336	ENST00000738200.1	n.226T>C		non_coding_transcript_exon_variant	Exon 2 of 3

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

GnomAD2 exomes AF: 0.255 AC: 29084 AN: 114128 AF XY: 0.268

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 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

African (AFR) AF: 0.164 AC: 1102 AN: 6738

American (AMR) AF: 0.183 AC: 3527 AN: 19254

Ashkenazi Jewish (ASJ) AF: 0.211 AC: 1436 AN: 6806

East Asian (EAS) AF: 0.506 AC: 4127 AN: 8162

South Asian (SAS) AF: 0.386 AC: 19691 AN: 51076

European-Finnish (FIN) AF: 0.158 AC: 4131 AN: 26166

Middle Eastern (MID) AF: 0.227 AC: 517 AN: 2278

European-Non Finnish (NFE) AF: 0.214 AC: 25863 AN: 120944

Other (OTH) AF: 0.238 AC: 2680 AN: 11250

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

African (AFR) AF: 0.175 AC: 7276 AN: 41512

American (AMR) AF: 0.229 AC: 3495 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.212 AC: 736 AN: 3468

East Asian (EAS) AF: 0.496 AC: 2564 AN: 5168

South Asian (SAS) AF: 0.407 AC: 1962 AN: 4826

European-Finnish (FIN) AF: 0.158 AC: 1674 AN: 10604

Middle Eastern (MID) AF: 0.245 AC: 72 AN: 294

European-Non Finnish (NFE) AF: 0.214 AC: 14523 AN: 67988

Other (OTH) AF: 0.263 AC: 556 AN: 2114

Alfa AF: 0.218 Hom.: 10983

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
PhyloP100		0.21

Splicing

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

Other links and lift over

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