13-25205291-G-C

Variant names:

• chr13-25205291-G-C
• rs7139545
• ENST00000435725.2:n.195+4810C>G

Variant summary

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

The ENST00000435725.2(LINC01076):​n.195+4810C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.681 in 152,136 control chromosomes in the GnomAD database, including 37,477 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 (37477 hom., cov: 33)
• Consequence: LINC01076 ENST00000435725.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0450
• Publications: 1 publications found

Genes affected

LINC01076 (HGNC:49119): (long intergenic non-protein coding RNA 1076)

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.802 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
LINC01076	ENST00000435725.2	n.195+4810C>G		intron_variant	Intron 1 of 1	3
LINC01076	ENST00000803520.1	n.299-12078C>G		intron_variant	Intron 1 of 1
LINC01076	ENST00000803521.1	n.541+3502C>G		intron_variant	Intron 3 of 3
LINC01076	ENST00000803522.1	n.336+4810C>G		intron_variant	Intron 2 of 2

Frequencies

GnomAD3 genomes AF: 0.682 AC: 103650 AN: 152018 Hom.: 37476 Cov.: 33

Gnomad AFR AF: 0.445

Gnomad AMI AF: 0.749

Gnomad AMR AF: 0.704

Gnomad ASJ AF: 0.775

Gnomad EAS AF: 0.412

Gnomad SAS AF: 0.673

Gnomad FIN AF: 0.864

Gnomad MID AF: 0.693

Gnomad NFE AF: 0.808

Gnomad OTH AF: 0.683

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

GnomAD4 genome AF: 0.681 AC: 103680 AN: 152136 Hom.: 37477 Cov.: 33 AF XY: 0.683 AC XY: 50766 AN XY: 74376

African (AFR) AF: 0.445 AC: 18435 AN: 41456

American (AMR) AF: 0.704 AC: 10766 AN: 15296

Ashkenazi Jewish (ASJ) AF: 0.775 AC: 2689 AN: 3468

East Asian (EAS) AF: 0.411 AC: 2126 AN: 5178

South Asian (SAS) AF: 0.675 AC: 3255 AN: 4822

European-Finnish (FIN) AF: 0.864 AC: 9151 AN: 10590

Middle Eastern (MID) AF: 0.684 AC: 201 AN: 294

European-Non Finnish (NFE) AF: 0.808 AC: 54926 AN: 68008

Other (OTH) AF: 0.686 AC: 1448 AN: 2112

Alfa AF: 0.687 Hom.: 2359

Bravo AF: 0.654

Asia WGS AF: 0.566 AC: 1968 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	1.1
DANN	Benign	0.49
PhyloP100		0.045

Splicing

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

Other links and lift over

dbSNP: rs7139545; hg19: chr13-25779429;