ENST00000526385.6:n.365-2850T>A

Variant names:

• chr11-97894142-A-T
• rs2851651
• ENST00000526385.6:n.365-2850T>A

Variant summary

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

The ENST00000526385.6(LINC02713):​n.365-2850T>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.678 in 151,938 control chromosomes in the GnomAD database, including 34,986 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 (34986 hom., cov: 31)
• Consequence: LINC02713 ENST00000526385.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.46
• Publications: 1 publications found

Genes affected

LINC02713 (HGNC:54230): (long intergenic non-protein coding RNA 2713)

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.769 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LINC02713	NR_183633.1	n.475-2850T>A		intron_variant	Intron 4 of 5

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC02713	ENST00000526385.6	n.365-2850T>A		intron_variant	Intron 3 of 4	3
LINC02713	ENST00000653025.2	n.710-2850T>A		intron_variant	Intron 5 of 6
LINC02713	ENST00000667368.2	n.485-2850T>A		intron_variant	Intron 4 of 5

Frequencies

GnomAD3 genomes AF: 0.678 AC: 102878 AN: 151820 Hom.: 34949 Cov.: 31

Gnomad AFR AF: 0.697

Gnomad AMI AF: 0.613

Gnomad AMR AF: 0.742

Gnomad ASJ AF: 0.607

Gnomad EAS AF: 0.789

Gnomad SAS AF: 0.716

Gnomad FIN AF: 0.643

Gnomad MID AF: 0.582

Gnomad NFE AF: 0.651

Gnomad OTH AF: 0.656

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

GnomAD4 genome AF: 0.678 AC: 102965 AN: 151938 Hom.: 34986 Cov.: 31 AF XY: 0.678 AC XY: 50357 AN XY: 74228

African (AFR) AF: 0.697 AC: 28886 AN: 41440

American (AMR) AF: 0.742 AC: 11327 AN: 15260

Ashkenazi Jewish (ASJ) AF: 0.607 AC: 2106 AN: 3472

East Asian (EAS) AF: 0.789 AC: 4067 AN: 5154

South Asian (SAS) AF: 0.715 AC: 3454 AN: 4828

European-Finnish (FIN) AF: 0.643 AC: 6764 AN: 10524

Middle Eastern (MID) AF: 0.571 AC: 168 AN: 294

European-Non Finnish (NFE) AF: 0.651 AC: 44243 AN: 67942

Other (OTH) AF: 0.658 AC: 1392 AN: 2114

Alfa AF: 0.585 Hom.: 1854

Bravo AF: 0.683

Asia WGS AF: 0.753 AC: 2617 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	0.41
DANN	Benign	0.38
PhyloP100		-1.5

Splicing

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

Other links and lift over

dbSNP: rs2851651; hg19: chr11-97765142;