rs183266

Variant names:

• chr14-77031632-C-A
• rs183266
• ENST00000693076.1:n.1626G>T

Your query was ambiguous. Multiple possible variants found:

• chr14-77031632-C-A
• chr14-77031632-C-G

Variant summary

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

The NR_169510.1(LOC105370579):​n.1951G>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 0.869 in 152,034 control chromosomes in the GnomAD database, including 57,524 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 0.87 (57523 hom., cov: 31)
  • Exomes 𝑓: 0.75 (1 hom.)
• Consequence: LOC105370579 NR_169510.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.23
• Publications: 11 publications found

Genes affected

ENSG00000289347 (HGNC:):

LINC02289 (HGNC:53205): (long intergenic non-protein coding RNA 2289)

LINC02288 (HGNC:27505): (long intergenic non-protein coding RNA 2288)

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.887 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NR_169510.1. 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
	LOC105370579	NR_169510.1		n.1951G>T		non_coding_transcript_exon	Exon 2 of 2
	LOC107984638	NR_190001.1		n.*60C>A		downstream_gene	N/A
	LOC107984638	NR_190002.1		n.*60C>A		downstream_gene	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000289347	ENST00000693076.1		n.1626G>T		non_coding_transcript_exon	Exon 2 of 2
	LINC02289	ENST00000716908.1		n.304+9422G>T		intron	N/A
	LINC02288	ENST00000793445.1		n.62+3821C>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.869 AC: 132083 AN: 151912 Hom.: 57495 Cov.: 31

Gnomad AFR AF: 0.850

Gnomad AMI AF: 0.867

Gnomad AMR AF: 0.818

Gnomad ASJ AF: 0.866

Gnomad EAS AF: 0.857

Gnomad SAS AF: 0.862

Gnomad FIN AF: 0.884

Gnomad MID AF: 0.867

Gnomad NFE AF: 0.893

Gnomad OTH AF: 0.859

GnomAD4 exome AF: 0.750 AC: 3 AN: 4 Hom.: 1 AF XY: 0.750 AC XY: 3 AN XY: 4

African (AFR) AC: 0 AN: 0

American (AMR) AC: 0 AN: 0

Ashkenazi Jewish (ASJ) AC: 0 AN: 0

East Asian (EAS) AC: 0 AN: 0

South Asian (SAS) AC: 0 AN: 0

European-Finnish (FIN) AC: 0 AN: 0

Middle Eastern (MID) AC: 0 AN: 0

European-Non Finnish (NFE) AF: 0.750 AC: 3 AN: 4

Other (OTH) AC: 0 AN: 0

GnomAD4 genome AF: 0.869 AC: 132167 AN: 152030 Hom.: 57523 Cov.: 31 AF XY: 0.867 AC XY: 64465 AN XY: 74332

African (AFR) AF: 0.849 AC: 35185 AN: 41426

American (AMR) AF: 0.818 AC: 12490 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.866 AC: 3007 AN: 3472

East Asian (EAS) AF: 0.857 AC: 4438 AN: 5178

South Asian (SAS) AF: 0.862 AC: 4146 AN: 4808

European-Finnish (FIN) AF: 0.884 AC: 9342 AN: 10562

Middle Eastern (MID) AF: 0.864 AC: 254 AN: 294

European-Non Finnish (NFE) AF: 0.893 AC: 60704 AN: 67998

Other (OTH) AF: 0.858 AC: 1810 AN: 2110

Alfa AF: 0.880 Hom.: 145394

Bravo AF: 0.864

Asia WGS AF: 0.867 AC: 3016 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	0.18
DANN	Benign	0.40
PhyloP100		-1.2

Splicing

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

Other links and lift over

dbSNP: rs183266; hg19: chr14-77497975;