rs31689

Variant names:

• chr5-159861445-C-T
• rs31689
• ENST00000522627.1:n.3691+5427G>A

Variant summary

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

The ENST00000522627.1(LINC01847):​n.3691+5427G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.709 in 152,082 control chromosomes in the GnomAD database, including 38,700 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 0.71 (38700 hom., cov: 32)
• Consequence: LINC01847 ENST00000522627.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.05
• Publications: 2 publications found

Genes affected

LINC01847 (HGNC:52662): (long intergenic non-protein coding RNA 1847)

ACMG classification

Our verdict: Benign. The variant received -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 = 0.795 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000522627.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC01847	NR_109891.1		n.3691+5427G>A		intron	N/A

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC01847	ENST00000522627.1	TSL:1	n.3691+5427G>A		intron	N/A
	LINC01847	ENST00000816795.1		n.489G>A		non_coding_transcript_exon	Exon 4 of 4
	LINC01847	ENST00000816796.1		n.278G>A		non_coding_transcript_exon	Exon 2 of 2

Frequencies

GnomAD3 genomes AF: 0.709 AC: 107731 AN: 151964 Hom.: 38649 Cov.: 32

Gnomad AFR AF: 0.797

Gnomad AMI AF: 0.649

Gnomad AMR AF: 0.682

Gnomad ASJ AF: 0.773

Gnomad EAS AF: 0.815

Gnomad SAS AF: 0.814

Gnomad FIN AF: 0.600

Gnomad MID AF: 0.822

Gnomad NFE AF: 0.660

Gnomad OTH AF: 0.707

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

GnomAD4 genome AF: 0.709 AC: 107839 AN: 152082 Hom.: 38700 Cov.: 32 AF XY: 0.709 AC XY: 52691 AN XY: 74342

African (AFR) AF: 0.798 AC: 33104 AN: 41508

American (AMR) AF: 0.682 AC: 10433 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.773 AC: 2682 AN: 3468

East Asian (EAS) AF: 0.815 AC: 4198 AN: 5150

South Asian (SAS) AF: 0.813 AC: 3918 AN: 4820

European-Finnish (FIN) AF: 0.600 AC: 6339 AN: 10566

Middle Eastern (MID) AF: 0.836 AC: 244 AN: 292

European-Non Finnish (NFE) AF: 0.660 AC: 44844 AN: 67966

Other (OTH) AF: 0.704 AC: 1486 AN: 2110

Alfa AF: 0.685 Hom.: 144163

Bravo AF: 0.718

Asia WGS AF: 0.796 AC: 2765 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.97
DANN	Benign	0.39
PhyloP100		-1.0

Splicing

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

Other links and lift over

dbSNP: rs31689; hg19: chr5-159288452; COSMIC: COSV73135781;