rs1917028

Positions:

• chr5-142747191-C-G
• chr5-142747191-C-T

Variant summary

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

The NR_110558.1(LINC01844):​n.119+1473C>G 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 0.33 in 152,128 control chromosomes in the GnomAD database, including 15,837 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 0.33 (15837 hom., cov: 32)
• Consequence: LINC01844 NR_110558.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.305

Genes affected

LINC01844 (HGNC:52660): (long intergenic non-protein coding RNA 1844)

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.815 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LINC01844	NR_110558.1	n.119+1473C>G		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
LINC01844	ENST00000655828.1	n.768+1473C>G		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.329 AC: 50028 AN: 152010 Hom.: 15779 Cov.: 32

Gnomad AFR AF: 0.822

Gnomad AMI AF: 0.0439

Gnomad AMR AF: 0.283

Gnomad ASJ AF: 0.140

Gnomad EAS AF: 0.371

Gnomad SAS AF: 0.280

Gnomad FIN AF: 0.113

Gnomad MID AF: 0.282

Gnomad NFE AF: 0.0880

Gnomad OTH AF: 0.297

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

GnomAD4 genome AF: 0.330 AC: 50137 AN: 152128 Hom.: 15837 Cov.: 32 AF XY: 0.330 AC XY: 24505 AN XY: 74354

Gnomad4 AFR AF: 0.823

Gnomad4 AMR AF: 0.282

Gnomad4 ASJ AF: 0.140

Gnomad4 EAS AF: 0.372

Gnomad4 SAS AF: 0.280

Gnomad4 FIN AF: 0.113

Gnomad4 NFE AF: 0.0880

Gnomad4 OTH AF: 0.296

Alfa AF: 0.216 Hom.: 1154

Bravo AF: 0.366

Asia WGS AF: 0.374 AC: 1302 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	6.0
DANN	Benign	0.72

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1917028; hg19: chr5-142126756;