rs2966480

Variant names:

• chr7-112651307-C-A
• rs2966480
• ENST00000453459.1:n.580+11089C>A

Variant summary

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

The ENST00000453459.1(LINC03076):​n.580+11089C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.77 in 151,922 control chromosomes in the GnomAD database, including 46,500 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 0.77 (46500 hom., cov: 32)
• Consequence: LINC03076 ENST00000453459.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.843
• Publications: 2 publications found

Genes affected

LINC03076 (HGNC:56656): (long intergenic non-protein coding RNA 3076)

LOC101928012 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.902 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC101928012	NR_110158.1	n.577+11089C>A		intron_variant	Intron 5 of 7

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC03076	ENST00000453459.1	n.580+11089C>A		intron_variant	Intron 5 of 7	1
LINC03076	ENST00000652784.1	n.480+15385C>A		intron_variant	Intron 4 of 6
LINC03076	ENST00000653349.1	n.593+11089C>A		intron_variant	Intron 5 of 6

Frequencies

GnomAD3 genomes AF: 0.770 AC: 116943 AN: 151804 Hom.: 46459 Cov.: 32

Gnomad AFR AF: 0.910

Gnomad AMI AF: 0.786

Gnomad AMR AF: 0.663

Gnomad ASJ AF: 0.791

Gnomad EAS AF: 0.221

Gnomad SAS AF: 0.622

Gnomad FIN AF: 0.760

Gnomad MID AF: 0.756

Gnomad NFE AF: 0.762

Gnomad OTH AF: 0.778

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

GnomAD4 genome AF: 0.770 AC: 117044 AN: 151922 Hom.: 46500 Cov.: 32 AF XY: 0.764 AC XY: 56723 AN XY: 74260

African (AFR) AF: 0.910 AC: 37786 AN: 41542

American (AMR) AF: 0.662 AC: 10099 AN: 15246

Ashkenazi Jewish (ASJ) AF: 0.791 AC: 2743 AN: 3466

East Asian (EAS) AF: 0.222 AC: 1146 AN: 5168

South Asian (SAS) AF: 0.623 AC: 3001 AN: 4818

European-Finnish (FIN) AF: 0.760 AC: 8047 AN: 10584

Middle Eastern (MID) AF: 0.765 AC: 225 AN: 294

European-Non Finnish (NFE) AF: 0.762 AC: 51638 AN: 67784

Other (OTH) AF: 0.779 AC: 1642 AN: 2108

Alfa AF: 0.764 Hom.: 22284

Bravo AF: 0.770

Asia WGS AF: 0.519 AC: 1805 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	0.98
DANN	Benign	0.41
PhyloP100		-0.84

Splicing

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

Other links and lift over

dbSNP: rs2966480; hg19: chr7-112291362;