ENST00000741042.1:n.347-11193C>T

Variant names:

• chr11-130819427-G-A
• rs7934985
• ENST00000741042.1:n.347-11193C>T

Variant summary

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

The ENST00000741042.1(LINC02551):​n.347-11193C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.404 in 151,086 control chromosomes in the GnomAD database, including 12,610 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 0.40 (12610 hom., cov: 31)
• Consequence: LINC02551 ENST00000741042.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.818
• Publications: 1 publications found

Genes affected

LINC02551 (HGNC:53586): (long intergenic non-protein coding RNA 2551)

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.76).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.439 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC02551	ENST00000741042.1	n.347-11193C>T		intron_variant	Intron 3 of 3

Frequencies

GnomAD3 genomes AF: 0.404 AC: 60966 AN: 150966 Hom.: 12609 Cov.: 31

Gnomad AFR AF: 0.325

Gnomad AMI AF: 0.553

Gnomad AMR AF: 0.353

Gnomad ASJ AF: 0.467

Gnomad EAS AF: 0.434

Gnomad SAS AF: 0.384

Gnomad FIN AF: 0.490

Gnomad MID AF: 0.444

Gnomad NFE AF: 0.443

Gnomad OTH AF: 0.414

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

GnomAD4 genome AF: 0.404 AC: 60999 AN: 151086 Hom.: 12610 Cov.: 31 AF XY: 0.406 AC XY: 29953 AN XY: 73806

African (AFR) AF: 0.325 AC: 13375 AN: 41112

American (AMR) AF: 0.353 AC: 5349 AN: 15166

Ashkenazi Jewish (ASJ) AF: 0.467 AC: 1616 AN: 3460

East Asian (EAS) AF: 0.434 AC: 2204 AN: 5082

South Asian (SAS) AF: 0.384 AC: 1832 AN: 4766

European-Finnish (FIN) AF: 0.490 AC: 5123 AN: 10458

Middle Eastern (MID) AF: 0.433 AC: 123 AN: 284

European-Non Finnish (NFE) AF: 0.443 AC: 30003 AN: 67754

Other (OTH) AF: 0.416 AC: 873 AN: 2098

Alfa AF: 0.404 Hom.: 1650

Bravo AF: 0.388

Asia WGS AF: 0.426 AC: 1479 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.76
CADD	Benign	2.4
DANN	Benign	0.82
PhyloP100		-0.82

Splicing

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

Other links and lift over

dbSNP: rs7934985; hg19: chr11-130689322;