rs2427393

Variant names:

• chr20-62694924-G-A
• rs2427393
• ENST00000435412.2:n.477C>T

Variant summary

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

The ENST00000435412.2(LINC00686):​n.477C>T 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 0.226 in 161,680 control chromosomes in the GnomAD database, including 4,281 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 0.23 (4062 hom., cov: 34)
  • Exomes 𝑓: 0.21 (219 hom.)
• Consequence: LINC00686 ENST00000435412.2 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.09
• Publications: 5 publications found

Genes affected

LINC00686 (HGNC:16221): (long intergenic non-protein coding RNA 686)

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.08).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.273 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000435412.2. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC00686	ENST00000435412.2	TSL:3	n.477C>T		non_coding_transcript_exon	Exon 2 of 2

Frequencies

GnomAD3 genomes AF: 0.227 AC: 34450 AN: 152092 Hom.: 4061 Cov.: 34

Gnomad AFR AF: 0.278

Gnomad AMI AF: 0.145

Gnomad AMR AF: 0.171

Gnomad ASJ AF: 0.202

Gnomad EAS AF: 0.261

Gnomad SAS AF: 0.246

Gnomad FIN AF: 0.214

Gnomad MID AF: 0.215

Gnomad NFE AF: 0.208

Gnomad OTH AF: 0.220

GnomAD4 exome AF: 0.213 AC: 2014 AN: 9470 Hom.: 219 AF XY: 0.216 AC XY: 1007 AN XY: 4660

African (AFR) AF: 0.203 AC: 15 AN: 74

American (AMR) AF: 0.00 AC: 0 AN: 8

Ashkenazi Jewish (ASJ) AF: 0.500 AC: 2 AN: 4

East Asian (EAS) AF: 0.00 AC: 0 AN: 4

South Asian (SAS) AF: 0.274 AC: 23 AN: 84

European-Finnish (FIN) AF: 0.215 AC: 1582 AN: 7342

Middle Eastern (MID) AF: 0.193 AC: 293 AN: 1516

European-Non Finnish (NFE) AF: 0.239 AC: 52 AN: 218

Other (OTH) AF: 0.214 AC: 47 AN: 220

GnomAD4 genome AF: 0.226 AC: 34454 AN: 152210 Hom.: 4062 Cov.: 34 AF XY: 0.226 AC XY: 16838 AN XY: 74412

African (AFR) AF: 0.277 AC: 11520 AN: 41540

American (AMR) AF: 0.171 AC: 2616 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.202 AC: 700 AN: 3468

East Asian (EAS) AF: 0.261 AC: 1355 AN: 5182

South Asian (SAS) AF: 0.246 AC: 1184 AN: 4822

European-Finnish (FIN) AF: 0.214 AC: 2268 AN: 10582

Middle Eastern (MID) AF: 0.197 AC: 58 AN: 294

European-Non Finnish (NFE) AF: 0.208 AC: 14163 AN: 68002

Other (OTH) AF: 0.216 AC: 458 AN: 2116

Alfa AF: 0.208 Hom.: 5778

Bravo AF: 0.223

Asia WGS AF: 0.237 AC: 826 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.1
CADD	Benign	0.68
DANN	Benign	0.57
PhyloP100		-1.1

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs2427393;

hg19: chr20-61326276;

COSMIC: COSV70961451;