rs4795885

chr17-34176523-G-Achr17-34176523-G-C

Variant summary

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

The NR_110748.1(LINC01989):n.730-1800C>T variant causes a intron, non coding transcript change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.876 in 152,156 control chromosomes in the GnomAD database, including 58,674 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 0.88 (58669 hom., cov: 31)
  • Exomes 𝑓: 0.79 (5 hom.)
• Consequence: LINC01989 NR_110748.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.661

Genes affected

LINC01989 (HGNC:52821): (long intergenic non-protein coding RNA 1989)

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.977 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LINC01989	NR_110748.1	n.730-1800C>T		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
LINC01989	ENST00000566930.6	n.730-1800C>T		intron_variant, non_coding_transcript_variant		1
LINC01989	ENST00000580792.1	n.119-6964C>T		intron_variant, non_coding_transcript_variant		3
LINC01989	ENST00000584724.5	n.85+6238C>T		intron_variant, non_coding_transcript_variant		3
	ENST00000579438.1			upstream_gene_variant

Frequencies

GnomAD3 genomes AF: 0.875 AC: 133088 AN: 152024 Hom.: 58603 Cov.: 31

Gnomad AFR AF: 0.969

Gnomad AMI AF: 0.916

Gnomad AMR AF: 0.872

Gnomad ASJ AF: 0.857

Gnomad EAS AF: 0.999

Gnomad SAS AF: 0.962

Gnomad FIN AF: 0.836

Gnomad MID AF: 0.867

Gnomad NFE AF: 0.811

Gnomad OTH AF: 0.860

GnomAD4 exome AF: 0.786 AC: 11 AN: 14 Hom.: 5 Cov.: 0 AF XY: 0.750 AC XY: 9 AN XY: 12

Gnomad4 FIN exome AF: 0.750

Gnomad4 NFE exome AF: 0.800

GnomAD4 genome AF: 0.876 AC: 133213 AN: 152142 Hom.: 58669 Cov.: 31 AF XY: 0.878 AC XY: 65253 AN XY: 74332

Gnomad4 AFR AF: 0.969

Gnomad4 AMR AF: 0.873

Gnomad4 ASJ AF: 0.857

Gnomad4 EAS AF: 0.999

Gnomad4 SAS AF: 0.963

Gnomad4 FIN AF: 0.836

Gnomad4 NFE AF: 0.811

Gnomad4 OTH AF: 0.861

Alfa AF: 0.857 Hom.: 8109

Bravo AF: 0.881

Asia WGS AF: 0.978 AC: 3403 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
Cadd	Benign	0.19
Dann	Benign	0.49

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4795885; hg19: chr17-32503542;