ENST00000418420.1:n.117-16728A>G

Variant names:

• chr2-14333831-T-C
• rs12616227
• ENST00000418420.1:n.117-16728A>G

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000418420.1(LINC00276):​n.117-16728A>G variant causes a intron 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 ENST00000418420.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.140
• Publications: 1 publications found

Genes affected

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

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt
LINC00276	NR_103814.2	n.117-16728A>G		intron_variant	Intron 1 of 3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC00276	ENST00000418420.1	n.117-16728A>G		intron_variant	Intron 1 of 3	1
LINC00276	ENST00000417751.5	n.122-16728A>G		intron_variant	Intron 1 of 4	2
LINC00276	ENST00000720689.1	n.249-16728A>G		intron_variant	Intron 1 of 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

African (AFR) AF: 0.633 AC: 26269 AN: 41496

American (AMR) AF: 0.602 AC: 9203 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.769 AC: 2667 AN: 3470

East Asian (EAS) AF: 0.548 AC: 2829 AN: 5164

South Asian (SAS) AF: 0.710 AC: 3417 AN: 4816

European-Finnish (FIN) AF: 0.746 AC: 7895 AN: 10582

Middle Eastern (MID) AF: 0.796 AC: 234 AN: 294

European-Non Finnish (NFE) AF: 0.718 AC: 48801 AN: 68004

Other (OTH) AF: 0.680 AC: 1435 AN: 2110

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
PhyloP100		-0.14

Splicing

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

Other links and lift over

dbSNP: rs12616227; hg19: chr2-14473955;