rs2966480

chr7-112651307-C-A

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NR_110158.1(LOC101928012):n.577+11089C>A variant causes a intron, non coding transcript 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: LOC101928012 NR_110158.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.843

Genes affected

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

LOC101928012 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	UniProt
LOC101928012	NR_110158.1	n.577+11089C>A		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
LINC03076	ENST00000656697.1	n.468+15385C>A		intron_variant, non_coding_transcript_variant

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

Gnomad4 AFR AF: 0.910

Gnomad4 AMR AF: 0.662

Gnomad4 ASJ AF: 0.791

Gnomad4 EAS AF: 0.222

Gnomad4 SAS AF: 0.623

Gnomad4 FIN AF: 0.760

Gnomad4 NFE AF: 0.762

Gnomad4 OTH AF: 0.779

Alfa AF: 0.763 Hom.: 19679

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2966480; hg19: chr7-112291362;