7-112522672-C-T

Variant names:

• chr7-112522672-C-T
• rs3095039
• ENST00000777765.1:n.219-45C>T

Variant summary

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

The ENST00000777765.1(LINC03076):​n.219-45C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.461 in 151,958 control chromosomes in the GnomAD database, including 17,751 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 0.46 (17751 hom., cov: 32)
• Consequence: LINC03076 ENST00000777765.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.165
• Publications: 6 publications found

Genes affected

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

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.853 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
LINC03076	ENST00000777765.1	n.219-45C>T		intron_variant	Intron 1 of 2

Frequencies

GnomAD3 genomes AF: 0.461 AC: 70000 AN: 151840 Hom.: 17729 Cov.: 32

Gnomad AFR AF: 0.614

Gnomad AMI AF: 0.258

Gnomad AMR AF: 0.493

Gnomad ASJ AF: 0.296

Gnomad EAS AF: 0.875

Gnomad SAS AF: 0.422

Gnomad FIN AF: 0.396

Gnomad MID AF: 0.329

Gnomad NFE AF: 0.355

Gnomad OTH AF: 0.416

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

GnomAD4 genome AF: 0.461 AC: 70075 AN: 151958 Hom.: 17751 Cov.: 32 AF XY: 0.463 AC XY: 34416 AN XY: 74256

African (AFR) AF: 0.614 AC: 25459 AN: 41442

American (AMR) AF: 0.492 AC: 7511 AN: 15266

Ashkenazi Jewish (ASJ) AF: 0.296 AC: 1026 AN: 3470

East Asian (EAS) AF: 0.875 AC: 4525 AN: 5174

South Asian (SAS) AF: 0.422 AC: 2031 AN: 4810

European-Finnish (FIN) AF: 0.396 AC: 4163 AN: 10522

Middle Eastern (MID) AF: 0.323 AC: 95 AN: 294

European-Non Finnish (NFE) AF: 0.355 AC: 24155 AN: 67956

Other (OTH) AF: 0.414 AC: 875 AN: 2112

Alfa AF: 0.425 Hom.: 2583

Bravo AF: 0.477

Asia WGS AF: 0.587 AC: 2040 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	6.7
DANN	Benign	0.61
PhyloP100		0.17

Splicing

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

Other links and lift over

dbSNP: rs3095039; hg19: chr7-112162727;