2-13726405-C-A

Variant names:

• chr2-13726405-C-A
• rs1446546
• ENST00000417751.5:n.405+12782G>T

Variant summary

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

The ENST00000417751.5(LINC00276):​n.405+12782G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0598 in 152,028 control chromosomes in the GnomAD database, including 564 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 0.060 (564 hom., cov: 32)
• Consequence: LINC00276 ENST00000417751.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.316
• Publications: 1 publications found

Genes affected

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

ENSG00000227718 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.296 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105373438	NR_188380.1	n.350-429C>A		intron_variant	Intron 3 of 4
LOC105373438	NR_188381.1	n.207-31154C>A		intron_variant	Intron 2 of 2
LOC105373438	NR_188382.1	n.207-18438C>A		intron_variant	Intron 2 of 3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC00276	ENST00000417751.5	n.405+12782G>T		intron_variant	Intron 4 of 4	2
ENSG00000227718	ENST00000420828.1	n.146-429C>A		intron_variant	Intron 1 of 2	2
LINC00276	ENST00000747982.1	n.52-15684G>T		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.0597 AC: 9067 AN: 151912 Hom.: 562 Cov.: 32

Gnomad AFR AF: 0.0436

Gnomad AMI AF: 0.0231

Gnomad AMR AF: 0.137

Gnomad ASJ AF: 0.147

Gnomad EAS AF: 0.308

Gnomad SAS AF: 0.0941

Gnomad FIN AF: 0.0329

Gnomad MID AF: 0.0506

Gnomad NFE AF: 0.0307

Gnomad OTH AF: 0.0705

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

GnomAD4 genome AF: 0.0598 AC: 9092 AN: 152028 Hom.: 564 Cov.: 32 AF XY: 0.0630 AC XY: 4679 AN XY: 74320

African (AFR) AF: 0.0439 AC: 1821 AN: 41508

American (AMR) AF: 0.138 AC: 2097 AN: 15230

Ashkenazi Jewish (ASJ) AF: 0.147 AC: 511 AN: 3472

East Asian (EAS) AF: 0.308 AC: 1590 AN: 5158

South Asian (SAS) AF: 0.0944 AC: 454 AN: 4810

European-Finnish (FIN) AF: 0.0329 AC: 349 AN: 10610

Middle Eastern (MID) AF: 0.0544 AC: 16 AN: 294

European-Non Finnish (NFE) AF: 0.0306 AC: 2082 AN: 67930

Other (OTH) AF: 0.0717 AC: 151 AN: 2106

Alfa AF: 0.0467 Hom.: 538

Bravo AF: 0.0700

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	0.36
DANN	Benign	0.55
PhyloP100		0.32

Splicing

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

Other links and lift over

dbSNP: rs1446546; hg19: chr2-13866530;