ENST00000443123.1:n.454C>T

Variant names:

• chr2-107266649-G-A
• rs7587131
• ENST00000443123.1:n.454C>T

Variant summary

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

The ENST00000443123.1(LINC01789):​n.454C>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 0.849 in 152,248 control chromosomes in the GnomAD database, including 55,023 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 0.85 (55012 hom., cov: 34)
  • Exomes 𝑓: 0.92 (11 hom.)
• Consequence: LINC01789 ENST00000443123.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.246
• Publications: 2 publications found

Genes affected

LINC01789 (HGNC:52578): (long intergenic non-protein coding RNA 1789)

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.82).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.942 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LINC01789	NR_183814.1	n.154C>T		non_coding_transcript_exon_variant	Exon 2 of 4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC01789	ENST00000443123.1	n.454C>T		non_coding_transcript_exon_variant	Exon 2 of 4	5
LINC01789	ENST00000455614.1	n.380C>T		non_coding_transcript_exon_variant	Exon 5 of 6	3

Frequencies

GnomAD3 genomes AF: 0.849 AC: 129198 AN: 152104 Hom.: 54990 Cov.: 34

Gnomad AFR AF: 0.818

Gnomad AMI AF: 0.685

Gnomad AMR AF: 0.867

Gnomad ASJ AF: 0.874

Gnomad EAS AF: 0.965

Gnomad SAS AF: 0.890

Gnomad FIN AF: 0.889

Gnomad MID AF: 0.851

Gnomad NFE AF: 0.847

Gnomad OTH AF: 0.867

GnomAD4 exome AF: 0.923 AC: 24 AN: 26 Hom.: 11 Cov.: 0 AF XY: 0.900 AC XY: 18 AN XY: 20

African (AFR) AF: 1.00 AC: 4 AN: 4

American (AMR) AC: 0 AN: 0

Ashkenazi Jewish (ASJ) AC: 0 AN: 0

East Asian (EAS) AC: 0 AN: 0

South Asian (SAS) AF: 1.00 AC: 2 AN: 2

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

Middle Eastern (MID) AC: 0 AN: 0

European-Non Finnish (NFE) AF: 0.875 AC: 14 AN: 16

Other (OTH) AF: 1.00 AC: 4 AN: 4

GnomAD4 genome AF: 0.849 AC: 129262 AN: 152222 Hom.: 55012 Cov.: 34 AF XY: 0.852 AC XY: 63433 AN XY: 74416

African (AFR) AF: 0.817 AC: 33934 AN: 41528

American (AMR) AF: 0.866 AC: 13255 AN: 15298

Ashkenazi Jewish (ASJ) AF: 0.874 AC: 3034 AN: 3472

East Asian (EAS) AF: 0.965 AC: 4989 AN: 5172

South Asian (SAS) AF: 0.889 AC: 4296 AN: 4830

European-Finnish (FIN) AF: 0.889 AC: 9432 AN: 10608

Middle Eastern (MID) AF: 0.861 AC: 253 AN: 294

European-Non Finnish (NFE) AF: 0.847 AC: 57618 AN: 68000

Other (OTH) AF: 0.866 AC: 1826 AN: 2108

Alfa AF: 0.851 Hom.: 68487

Bravo AF: 0.847

Asia WGS AF: 0.905 AC: 3149 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	4.5
DANN	Benign	0.75
PhyloP100		-0.25

Splicing

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

Other links and lift over

dbSNP: rs7587131; hg19: chr2-107883105;