chr7-84515886-A-C

Variant names:

• chr7-84515886-A-C
• rs11766001
• ENST00000446000.2:n.82+13352A>C

Variant summary

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

The ENST00000446000.2(LINC03017):​n.82+13352A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.108 in 151,972 control chromosomes in the GnomAD database, including 1,131 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 0.11 (1131 hom., cov: 32)
• Consequence: LINC03017 ENST00000446000.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.69
• Publications: 16 publications found

Genes affected

LINC03017 (HGNC:56146): (long intergenic non-protein coding RNA 3017)

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.152 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
LINC03017	ENST00000446000.2	n.82+13352A>C		intron_variant	Intron 1 of 3	3

Frequencies

GnomAD3 genomes AF: 0.108 AC: 16470 AN: 151854 Hom.: 1131 Cov.: 32

Gnomad AFR AF: 0.0427

Gnomad AMI AF: 0.156

Gnomad AMR AF: 0.0967

Gnomad ASJ AF: 0.185

Gnomad EAS AF: 0.000581

Gnomad SAS AF: 0.0957

Gnomad FIN AF: 0.113

Gnomad MID AF: 0.158

Gnomad NFE AF: 0.154

Gnomad OTH AF: 0.131

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

GnomAD4 genome AF: 0.108 AC: 16466 AN: 151972 Hom.: 1131 Cov.: 32 AF XY: 0.106 AC XY: 7854 AN XY: 74288

African (AFR) AF: 0.0426 AC: 1770 AN: 41520

American (AMR) AF: 0.0963 AC: 1466 AN: 15218

Ashkenazi Jewish (ASJ) AF: 0.185 AC: 640 AN: 3468

East Asian (EAS) AF: 0.000582 AC: 3 AN: 5152

South Asian (SAS) AF: 0.0966 AC: 466 AN: 4826

European-Finnish (FIN) AF: 0.113 AC: 1201 AN: 10604

Middle Eastern (MID) AF: 0.160 AC: 47 AN: 294

European-Non Finnish (NFE) AF: 0.154 AC: 10457 AN: 67870

Other (OTH) AF: 0.130 AC: 274 AN: 2108

Alfa AF: 0.105 Hom.: 590

Bravo AF: 0.103

Asia WGS AF: 0.0420 AC: 146 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	10
DANN	Benign	0.77
PhyloP100		1.7

Splicing

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

Other links and lift over

dbSNP: rs11766001; hg19: chr7-84145202;