rs7732591

chr5-142745612-T-C

Variant summary

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

The NR_110558.1(LINC01844):n.13T>C 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 0.225 in 398,052 control chromosomes in the GnomAD database, including 21,703 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 (15822 hom., cov: 32)
  • Exomes 𝑓: 0.16 (5881 hom.)
• Consequence: LINC01844 NR_110558.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.162

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=-0.87).
• 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	UniProt
LINC01844	NR_110558.1	n.13T>C		non_coding_transcript_exon_variant	1/4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
LINC01844	ENST00000655828.1	n.662T>C		non_coding_transcript_exon_variant	3/6

Frequencies

GnomAD3 genomes AF: 0.329 AC: 49958 AN: 151968 Hom.: 15761 Cov.: 32

Gnomad AFR AF: 0.822

Gnomad AMI AF: 0.0440

Gnomad AMR AF: 0.282

Gnomad ASJ AF: 0.140

Gnomad EAS AF: 0.373

Gnomad SAS AF: 0.281

Gnomad FIN AF: 0.113

Gnomad MID AF: 0.282

Gnomad NFE AF: 0.0875

Gnomad OTH AF: 0.297

GnomAD4 exome AF: 0.160 AC: 39420 AN: 245966 Hom.: 5881 Cov.: 0 AF XY: 0.154 AC XY: 19201 AN XY: 124624

Gnomad4 AFR exome AF: 0.808

Gnomad4 AMR exome AF: 0.279

Gnomad4 ASJ exome AF: 0.151

Gnomad4 EAS exome AF: 0.365

Gnomad4 SAS exome AF: 0.268

Gnomad4 FIN exome AF: 0.107

Gnomad4 NFE exome AF: 0.0941

Gnomad4 OTH exome AF: 0.221

GnomAD4 genome AF: 0.329 AC: 50070 AN: 152086 Hom.: 15822 Cov.: 32 AF XY: 0.329 AC XY: 24465 AN XY: 74352

Gnomad4 AFR AF: 0.823

Gnomad4 AMR AF: 0.281

Gnomad4 ASJ AF: 0.140

Gnomad4 EAS AF: 0.374

Gnomad4 SAS AF: 0.280

Gnomad4 FIN AF: 0.113

Gnomad4 NFE AF: 0.0875

Gnomad4 OTH AF: 0.295

Alfa AF: 0.140 Hom.: 6836

Bravo AF: 0.366

Asia WGS AF: 0.376 AC: 1309 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
Cadd	Benign	7.7
Dann	Benign	0.79

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7732591; hg19: chr5-142125177;