11-97908041-A-T

Variant names:

• chr11-97908041-A-T
• rs2597565
• ENST00000526385.6:n.365-16749T>A

Variant summary

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

The ENST00000526385.6(LINC02713):​n.365-16749T>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.579 in 152,048 control chromosomes in the GnomAD database, including 26,104 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 0.58 (26104 hom., cov: 32)
• Consequence: LINC02713 ENST00000526385.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.329
• Publications: 0 publications found

Genes affected

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

ENSG00000254555 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.715 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LINC02713	NR_183633.1	n.474+10797T>A		intron_variant	Intron 4 of 5

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC02713	ENST00000526385.6	n.365-16749T>A		intron_variant	Intron 3 of 4	3
LINC02713	ENST00000653025.2	n.709+8648T>A		intron_variant	Intron 5 of 6
LINC02713	ENST00000667368.2	n.484+10797T>A		intron_variant	Intron 4 of 5
ENSG00000254555	ENST00000524605.1	n.*212T>A		downstream_gene_variant		6

Frequencies

GnomAD3 genomes AF: 0.580 AC: 88054 AN: 151930 Hom.: 26086 Cov.: 32

Gnomad AFR AF: 0.662

Gnomad AMI AF: 0.556

Gnomad AMR AF: 0.669

Gnomad ASJ AF: 0.462

Gnomad EAS AF: 0.734

Gnomad SAS AF: 0.643

Gnomad FIN AF: 0.513

Gnomad MID AF: 0.443

Gnomad NFE AF: 0.511

Gnomad OTH AF: 0.556

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

GnomAD4 genome AF: 0.579 AC: 88105 AN: 152048 Hom.: 26104 Cov.: 32 AF XY: 0.582 AC XY: 43238 AN XY: 74334

African (AFR) AF: 0.662 AC: 27446 AN: 41476

American (AMR) AF: 0.669 AC: 10232 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.462 AC: 1604 AN: 3472

East Asian (EAS) AF: 0.734 AC: 3796 AN: 5170

South Asian (SAS) AF: 0.642 AC: 3096 AN: 4820

European-Finnish (FIN) AF: 0.513 AC: 5416 AN: 10548

Middle Eastern (MID) AF: 0.425 AC: 125 AN: 294

European-Non Finnish (NFE) AF: 0.511 AC: 34712 AN: 67958

Other (OTH) AF: 0.555 AC: 1172 AN: 2112

Alfa AF: 0.556 Hom.: 2916

Bravo AF: 0.593

Asia WGS AF: 0.678 AC: 2358 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	2.2
DANN	Benign	0.44
PhyloP100		0.33

Splicing

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

Other links and lift over

dbSNP: rs2597565; hg19: chr11-97779041;