7-112603259-G-C

Variant names:

• chr7-112603259-G-C
• rs43077
• ENST00000777765.1:n.267-17149G>C

Variant summary

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

The ENST00000777765.1(LINC03076):​n.267-17149G>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.478 in 151,698 control chromosomes in the GnomAD database, including 17,722 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 0.48 (17722 hom., cov: 31)
• Consequence: LINC03076 ENST00000777765.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.539
• Publications: 2 publications found

Genes affected

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

ENSG00000301323 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.517 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.267-17149G>C		intron_variant	Intron 2 of 2
LINC03076	ENST00000777766.1	n.388-17149G>C		intron_variant	Intron 1 of 1
ENSG00000301323	ENST00000778011.1	n.219-5890C>G		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.478 AC: 72392 AN: 151582 Hom.: 17714 Cov.: 31

Gnomad AFR AF: 0.463

Gnomad AMI AF: 0.538

Gnomad AMR AF: 0.467

Gnomad ASJ AF: 0.451

Gnomad EAS AF: 0.151

Gnomad SAS AF: 0.377

Gnomad FIN AF: 0.483

Gnomad MID AF: 0.326

Gnomad NFE AF: 0.521

Gnomad OTH AF: 0.461

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

GnomAD4 genome AF: 0.478 AC: 72451 AN: 151698 Hom.: 17722 Cov.: 31 AF XY: 0.473 AC XY: 35048 AN XY: 74146

African (AFR) AF: 0.463 AC: 19132 AN: 41280

American (AMR) AF: 0.467 AC: 7116 AN: 15240

Ashkenazi Jewish (ASJ) AF: 0.451 AC: 1564 AN: 3470

East Asian (EAS) AF: 0.151 AC: 776 AN: 5150

South Asian (SAS) AF: 0.375 AC: 1804 AN: 4806

European-Finnish (FIN) AF: 0.483 AC: 5090 AN: 10542

Middle Eastern (MID) AF: 0.347 AC: 102 AN: 294

European-Non Finnish (NFE) AF: 0.521 AC: 35410 AN: 67906

Other (OTH) AF: 0.461 AC: 970 AN: 2104

Alfa AF: 0.381 Hom.: 1041

Bravo AF: 0.476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	0.18
DANN	Benign	0.30
PhyloP100		-0.54

Splicing

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

Other links and lift over

dbSNP: rs43077; hg19: chr7-112243314;