rs1454183

Positions:

• chr2-13844585-G-A
• chr2-13844585-G-T

Variant summary

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

The ENST00000417751.5(LINC00276):​n.257-2971C>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 0.24 in 151,982 control chromosomes in the GnomAD database, including 5,724 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 0.24 (5724 hom., cov: 32)
• Consequence: LINC00276 ENST00000417751.5 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.746

Genes affected

LINC00276 (HGNC:38663): (long intergenic non-protein coding RNA 276)

LOC107985854 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.448 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LOC107985854	XR_001739296.1	n.95+6629G>A		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
LINC00276	ENST00000417751.5	n.257-2971C>T		intron_variant, non_coding_transcript_variant		2

Frequencies

GnomAD3 genomes AF: 0.239 AC: 36368 AN: 151864 Hom.: 5691 Cov.: 32

Gnomad AFR AF: 0.431

Gnomad AMI AF: 0.172

Gnomad AMR AF: 0.161

Gnomad ASJ AF: 0.177

Gnomad EAS AF: 0.463

Gnomad SAS AF: 0.281

Gnomad FIN AF: 0.167

Gnomad MID AF: 0.149

Gnomad NFE AF: 0.137

Gnomad OTH AF: 0.215

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

GnomAD4 genome AF: 0.240 AC: 36457 AN: 151982 Hom.: 5724 Cov.: 32 AF XY: 0.242 AC XY: 17948 AN XY: 74276

Gnomad4 AFR AF: 0.432

Gnomad4 AMR AF: 0.160

Gnomad4 ASJ AF: 0.177

Gnomad4 EAS AF: 0.464

Gnomad4 SAS AF: 0.281

Gnomad4 FIN AF: 0.167

Gnomad4 NFE AF: 0.137

Gnomad4 OTH AF: 0.221

Alfa AF: 0.188 Hom.: 566

Bravo AF: 0.248

Asia WGS AF: 0.391 AC: 1357 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	0.66
DANN	Benign	0.59

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1454183; hg19: chr2-13984710;