rs2427399

Variant names:

• chr20-62700093-G-A
• rs2427399
• ENST00000435412.2:n.137+296C>T

Your query was ambiguous. Multiple possible variants found:

• chr20-62700093-G-A
• chr20-62700093-G-T

Variant summary

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

The ENST00000435412.2(LINC00686):​n.137+296C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.235 in 152,254 control chromosomes in the GnomAD database, including 4,828 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 (4828 hom., cov: 34)
• Consequence: LINC00686 ENST00000435412.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0480
• Publications: 7 publications found

Genes affected

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

ENSG00000294525 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.28 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

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

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC00686	ENST00000435412.2	TSL:3	n.137+296C>T		intron	N/A
	ENSG00000294525	ENST00000724111.1		n.153-148G>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.235 AC: 35739 AN: 152136 Hom.: 4822 Cov.: 34

Gnomad AFR AF: 0.113

Gnomad AMI AF: 0.213

Gnomad AMR AF: 0.220

Gnomad ASJ AF: 0.275

Gnomad EAS AF: 0.238

Gnomad SAS AF: 0.230

Gnomad FIN AF: 0.411

Gnomad MID AF: 0.266

Gnomad NFE AF: 0.284

Gnomad OTH AF: 0.228

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.235 AC: 35754 AN: 152254 Hom.: 4828 Cov.: 34 AF XY: 0.240 AC XY: 17855 AN XY: 74432

African (AFR) AF: 0.112 AC: 4673 AN: 41564

American (AMR) AF: 0.220 AC: 3367 AN: 15296

Ashkenazi Jewish (ASJ) AF: 0.275 AC: 951 AN: 3462

East Asian (EAS) AF: 0.238 AC: 1232 AN: 5178

South Asian (SAS) AF: 0.231 AC: 1117 AN: 4828

European-Finnish (FIN) AF: 0.411 AC: 4353 AN: 10598

Middle Eastern (MID) AF: 0.276 AC: 81 AN: 294

European-Non Finnish (NFE) AF: 0.284 AC: 19303 AN: 68010

Other (OTH) AF: 0.228 AC: 483 AN: 2114

Alfa AF: 0.267 Hom.: 21571

Bravo AF: 0.217

Asia WGS AF: 0.210 AC: 730 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	5.4
DANN	Benign	0.88
PhyloP100		-0.048

Splicing

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

Other links and lift over

dbSNP: rs2427399; hg19: chr20-61331445;