13-25214448-T-C

Variant names:

• chr13-25214448-T-C
• rs4769414
• ENST00000803520.1:n.299-21235A>G

Variant summary

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

The ENST00000803520.1(LINC01076):​n.299-21235A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.666 in 151,884 control chromosomes in the GnomAD database, including 34,949 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 0.67 (34949 hom., cov: 30)
• Consequence: LINC01076 ENST00000803520.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.40
• Publications: 2 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=-1.05).
• BA1: GnomAd4 highest subpopulation (NFE) 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

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC01076	ENST00000803520.1	n.299-21235A>G		intron_variant	Intron 1 of 1
LINC01076	ENST00000803521.1	n.275-4157A>G		intron_variant	Intron 1 of 3

Frequencies

GnomAD3 genomes AF: 0.666 AC: 101032 AN: 151766 Hom.: 34926 Cov.: 30

Gnomad AFR AF: 0.501

Gnomad AMI AF: 0.920

Gnomad AMR AF: 0.543

Gnomad ASJ AF: 0.774

Gnomad EAS AF: 0.570

Gnomad SAS AF: 0.671

Gnomad FIN AF: 0.763

Gnomad MID AF: 0.741

Gnomad NFE AF: 0.775

Gnomad OTH AF: 0.681

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

GnomAD4 genome AF: 0.666 AC: 101090 AN: 151884 Hom.: 34949 Cov.: 30 AF XY: 0.662 AC XY: 49155 AN XY: 74250

African (AFR) AF: 0.502 AC: 20742 AN: 41340

American (AMR) AF: 0.542 AC: 8279 AN: 15264

Ashkenazi Jewish (ASJ) AF: 0.774 AC: 2684 AN: 3466

East Asian (EAS) AF: 0.569 AC: 2945 AN: 5172

South Asian (SAS) AF: 0.671 AC: 3222 AN: 4800

European-Finnish (FIN) AF: 0.763 AC: 8047 AN: 10552

Middle Eastern (MID) AF: 0.748 AC: 220 AN: 294

European-Non Finnish (NFE) AF: 0.775 AC: 52674 AN: 67970

Other (OTH) AF: 0.680 AC: 1438 AN: 2114

Alfa AF: 0.734 Hom.: 65698

Bravo AF: 0.638

Asia WGS AF: 0.614 AC: 2134 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.1
CADD	Benign	0.53
DANN	Benign	0.35
PhyloP100		-1.4

Splicing

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

Other links and lift over

dbSNP: rs4769414; hg19: chr13-25788586; COSMIC: COSV71236728;