ENST00000653901.1:n.112-15474A>G

Variant names:

• chr13-78807966-T-C
• rs9574309
• ENST00000653901.1:n.112-15474A>G

Variant summary

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

The ENST00000653901.1(LINC00331):​n.112-15474A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.45 in 151,692 control chromosomes in the GnomAD database, including 15,661 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 0.45 (15661 hom., cov: 32)
• Consequence: LINC00331 ENST00000653901.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.980
• Publications: 7 publications found

Genes affected

LINC00331 (HGNC:42048): (long intergenic non-protein coding RNA 331)

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.01).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.502 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LINC00331	NR_046869.2	n.225-15664A>G		intron_variant	Intron 2 of 4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC00331	ENST00000653901.1	n.112-15474A>G		intron_variant	Intron 1 of 4
LINC00331	ENST00000655539.2	n.225-15664A>G		intron_variant	Intron 2 of 5
LINC00331	ENST00000658469.1	n.225-11867A>G		intron_variant	Intron 2 of 7

Frequencies

GnomAD3 genomes AF: 0.450 AC: 68140 AN: 151574 Hom.: 15638 Cov.: 32

Gnomad AFR AF: 0.508

Gnomad AMI AF: 0.326

Gnomad AMR AF: 0.507

Gnomad ASJ AF: 0.458

Gnomad EAS AF: 0.462

Gnomad SAS AF: 0.387

Gnomad FIN AF: 0.378

Gnomad MID AF: 0.478

Gnomad NFE AF: 0.417

Gnomad OTH AF: 0.454

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

GnomAD4 genome AF: 0.450 AC: 68199 AN: 151692 Hom.: 15661 Cov.: 32 AF XY: 0.449 AC XY: 33265 AN XY: 74140

African (AFR) AF: 0.508 AC: 21046 AN: 41434

American (AMR) AF: 0.507 AC: 7728 AN: 15252

Ashkenazi Jewish (ASJ) AF: 0.458 AC: 1590 AN: 3468

East Asian (EAS) AF: 0.461 AC: 2384 AN: 5172

South Asian (SAS) AF: 0.386 AC: 1855 AN: 4808

European-Finnish (FIN) AF: 0.378 AC: 3983 AN: 10538

Middle Eastern (MID) AF: 0.479 AC: 140 AN: 292

European-Non Finnish (NFE) AF: 0.417 AC: 28215 AN: 67708

Other (OTH) AF: 0.456 AC: 961 AN: 2108

Alfa AF: 0.432 Hom.: 55443

Bravo AF: 0.464

Asia WGS AF: 0.456 AC: 1580 AN: 3472

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	1.5
DANN	Benign	0.46
PhyloP100		-0.98

Splicing

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

Other links and lift over

dbSNP: rs9574309; hg19: chr13-79382101;