rs740044

Positions:

• chr2-101983707-A-C
• chr2-101983707-A-G
• chr2-101983707-A-T

Variant summary

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

The NR_103791.1(LINC01127):​n.130A>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 0.799 in 152,214 control chromosomes in the GnomAD database, including 49,562 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 0.80 (49561 hom., cov: 33)
  • Exomes 𝑓: 1.0 (1 hom.)
• Consequence: LINC01127 NR_103791.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.964

Genes affected

LINC01127 (HGNC:49292): (long intergenic non-protein coding RNA 1127)

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.975 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LINC01127	NR_103791.1	n.130A>C		non_coding_transcript_exon_variant	2/4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
LINC01127	ENST00000627215.1	n.267A>C		non_coding_transcript_exon_variant	3/3	2

Frequencies

GnomAD3 genomes AF: 0.799 AC: 121508 AN: 152094 Hom.: 49500 Cov.: 33

Gnomad AFR AF: 0.945

Gnomad AMI AF: 0.650

Gnomad AMR AF: 0.788

Gnomad ASJ AF: 0.648

Gnomad EAS AF: 0.997

Gnomad SAS AF: 0.812

Gnomad FIN AF: 0.835

Gnomad MID AF: 0.696

Gnomad NFE AF: 0.702

Gnomad OTH AF: 0.768

GnomAD4 exome AF: 1.00 AC: 2 AN: 2 Hom.: 1 Cov.: 0 AF XY: 1.00 AC XY: 2 AN XY: 2

Gnomad4 NFE exome AF: 1.00

GnomAD4 genome AF: 0.799 AC: 121626 AN: 152212 Hom.: 49561 Cov.: 33 AF XY: 0.805 AC XY: 59898 AN XY: 74402

Gnomad4 AFR AF: 0.945

Gnomad4 AMR AF: 0.788

Gnomad4 ASJ AF: 0.648

Gnomad4 EAS AF: 0.997

Gnomad4 SAS AF: 0.810

Gnomad4 FIN AF: 0.835

Gnomad4 NFE AF: 0.702

Gnomad4 OTH AF: 0.772

Alfa AF: 0.712 Hom.: 15157

Bravo AF: 0.803

Asia WGS AF: 0.921 AC: 3205 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	1.1
DANN	Benign	0.42

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs740044; hg19: chr2-102600169;