rs2073383

Variant names:

• chr22-23459984-T-C
• rs2073383
• ENST00000786107.1:n.206T>C

Variant summary

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

The ENST00000786107.1(LINC01659):​n.206T>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 0.581 in 151,836 control chromosomes in the GnomAD database, including 25,745 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 0.58 (25745 hom., cov: 32)
• Consequence: LINC01659 ENST00000786107.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.04
• Publications: 4 publications found

Genes affected

LINC01659 (HGNC:52447): (long intergenic non-protein coding RNA 1659)

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.03).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.602 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC01659	ENST00000786107.1	n.206T>C		non_coding_transcript_exon_variant	Exon 1 of 2
LINC01659	ENST00000428415.2	n.1312-369T>C		intron_variant	Intron 2 of 2	2
LINC01659	ENST00000449711.2	n.930-369T>C		intron_variant	Intron 3 of 3	3

Frequencies

GnomAD3 genomes AF: 0.581 AC: 88118 AN: 151718 Hom.: 25722 Cov.: 32

Gnomad AFR AF: 0.608

Gnomad AMI AF: 0.465

Gnomad AMR AF: 0.578

Gnomad ASJ AF: 0.628

Gnomad EAS AF: 0.602

Gnomad SAS AF: 0.569

Gnomad FIN AF: 0.590

Gnomad MID AF: 0.636

Gnomad NFE AF: 0.561

Gnomad OTH AF: 0.588

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

GnomAD4 genome AF: 0.581 AC: 88195 AN: 151836 Hom.: 25745 Cov.: 32 AF XY: 0.585 AC XY: 43438 AN XY: 74194

African (AFR) AF: 0.608 AC: 25164 AN: 41396

American (AMR) AF: 0.578 AC: 8837 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.628 AC: 2178 AN: 3468

East Asian (EAS) AF: 0.601 AC: 3081 AN: 5128

South Asian (SAS) AF: 0.569 AC: 2740 AN: 4814

European-Finnish (FIN) AF: 0.590 AC: 6221 AN: 10538

Middle Eastern (MID) AF: 0.626 AC: 184 AN: 294

European-Non Finnish (NFE) AF: 0.561 AC: 38119 AN: 67894

Other (OTH) AF: 0.590 AC: 1248 AN: 2114

Alfa AF: 0.753 Hom.: 9791

Bravo AF: 0.581

Asia WGS AF: 0.579 AC: 2009 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	1.5
DANN	Benign	0.63
PhyloP100		-1.0

Splicing

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

Other links and lift over

dbSNP: rs2073383; hg19: chr22-23802171;