rs528301

Positions:

• chr2-44927769-G-A
• chr2-44927769-G-C
• chr2-44927769-G-T

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_Moderate BA1

The NR_147195.1(LINC01833):​n.378-4190C>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 0.718 in 152,178 control chromosomes in the GnomAD database, including 40,960 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 0.72 (40959 hom., cov: 34)
  • Exomes 𝑓: 1.0 (1 hom.)
• Consequence: LINC01833 NR_147195.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.45

Genes affected

LINC01833 (HGNC:52644): (long intergenic non-protein coding RNA 1833)

ACMG classification

Verdict is Benign. Variant got -10 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.43).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.962 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LINC01833	NR_147195.1	n.378-4190C>T		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
LINC01833	ENST00000437916.2	n.378-4190C>T		intron_variant, non_coding_transcript_variant		3
LINC01833	ENST00000432125.2	n.366-4190C>T		intron_variant, non_coding_transcript_variant		3

Frequencies

GnomAD3 genomes AF: 0.718 AC: 109125 AN: 152058 Hom.: 40896 Cov.: 34

Gnomad AFR AF: 0.914

Gnomad AMI AF: 0.663

Gnomad AMR AF: 0.754

Gnomad ASJ AF: 0.660

Gnomad EAS AF: 0.985

Gnomad SAS AF: 0.855

Gnomad FIN AF: 0.646

Gnomad MID AF: 0.731

Gnomad NFE AF: 0.575

Gnomad OTH AF: 0.686

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

Gnomad4 FIN exome AF: 1.00

GnomAD4 genome AF: 0.718 AC: 109250 AN: 152176 Hom.: 40959 Cov.: 34 AF XY: 0.725 AC XY: 53969 AN XY: 74390

Gnomad4 AFR AF: 0.915

Gnomad4 AMR AF: 0.754

Gnomad4 ASJ AF: 0.660

Gnomad4 EAS AF: 0.985

Gnomad4 SAS AF: 0.853

Gnomad4 FIN AF: 0.646

Gnomad4 NFE AF: 0.575

Gnomad4 OTH AF: 0.689

Alfa AF: 0.602 Hom.: 36979

Bravo AF: 0.735

Asia WGS AF: 0.899 AC: 3123 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.43
CADD	Benign	14
DANN	Benign	0.69

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs528301; hg19: chr2-45154908;