rs7587131

chr2-107266649-G-Achr2-107266649-G-Cchr2-107266649-G-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NR_183814.1(LINC01789):n.154C>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 NR_183814.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.246

Genes affected

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

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	UniProt
LINC01789	NR_183814.1	n.154C>T		non_coding_transcript_exon_variant	2/4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
LINC01789	ENST00000443123.1	n.454C>T		non_coding_transcript_exon_variant	2/4	5
LINC01789	ENST00000455614.1	n.380C>T		non_coding_transcript_exon_variant	5/6	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

Gnomad4 AFR exome AF: 1.00

Gnomad4 SAS exome AF: 1.00

Gnomad4 NFE exome AF: 0.875

Gnomad4 OTH exome AF: 1.00

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

Gnomad4 AFR AF: 0.817

Gnomad4 AMR AF: 0.866

Gnomad4 ASJ AF: 0.874

Gnomad4 EAS AF: 0.965

Gnomad4 SAS AF: 0.889

Gnomad4 FIN AF: 0.889

Gnomad4 NFE AF: 0.847

Gnomad4 OTH AF: 0.866

Alfa AF: 0.853 Hom.: 51753

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7587131; hg19: chr2-107883105;