rs12616227

chr2-14333831-T-C

Variant summary

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

The NR_103814.2(LINC00276):n.117-16728A>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 0.68 in 152,126 control chromosomes in the GnomAD database, including 35,494 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 0.68 (35494 hom., cov: 33)
• Consequence: LINC00276 NR_103814.2 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.140

Genes affected

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

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.04).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.712 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LINC00276	NR_103814.2	n.117-16728A>G		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
LINC00276	ENST00000417751.5	n.122-16728A>G		intron_variant, non_coding_transcript_variant		2
LINC00276	ENST00000418420.1	n.117-16728A>G		intron_variant, non_coding_transcript_variant		1

Frequencies

GnomAD3 genomes AF: 0.680 AC: 103436 AN: 152008 Hom.: 35478 Cov.: 33

Gnomad AFR AF: 0.634

Gnomad AMI AF: 0.809

Gnomad AMR AF: 0.603

Gnomad ASJ AF: 0.769

Gnomad EAS AF: 0.547

Gnomad SAS AF: 0.709

Gnomad FIN AF: 0.746

Gnomad MID AF: 0.794

Gnomad NFE AF: 0.718

Gnomad OTH AF: 0.684

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

GnomAD4 genome AF: 0.680 AC: 103488 AN: 152126 Hom.: 35494 Cov.: 33 AF XY: 0.678 AC XY: 50445 AN XY: 74350

Gnomad4 AFR AF: 0.633

Gnomad4 AMR AF: 0.602

Gnomad4 ASJ AF: 0.769

Gnomad4 EAS AF: 0.548

Gnomad4 SAS AF: 0.710

Gnomad4 FIN AF: 0.746

Gnomad4 NFE AF: 0.718

Gnomad4 OTH AF: 0.680

Alfa AF: 0.682 Hom.: 5612

Bravo AF: 0.666

Asia WGS AF: 0.617 AC: 2147 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
Cadd	Benign	2.7
Dann	Benign	0.53

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs12616227; hg19: chr2-14473955;