rs9380006

Variant names:

• chr6-27688720-A-C
• rs9380006
• ENST00000783746.1:n.860+218A>C

Variant summary

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

The ENST00000783746.1(LINC01012):​n.860+218A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.256 in 151,652 control chromosomes in the GnomAD database, including 5,898 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 0.26 (5898 hom., cov: 30)
• Consequence: LINC01012 ENST00000783746.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.583
• Publications: 8 publications found

Genes affected

LINC01012 (HGNC:48986): (long intergenic non-protein coding RNA 1012)

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.407 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000783746.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC01012	ENST00000783746.1		n.860+218A>C		intron	N/A
	LINC01012	ENST00000783747.1		n.516+218A>C		intron	N/A
	LINC01012	ENST00000783805.1		n.*94A>C		downstream_gene	N/A

Frequencies

GnomAD3 genomes AF: 0.255 AC: 38714 AN: 151532 Hom.: 5887 Cov.: 30

Gnomad AFR AF: 0.413

Gnomad AMI AF: 0.160

Gnomad AMR AF: 0.228

Gnomad ASJ AF: 0.108

Gnomad EAS AF: 0.364

Gnomad SAS AF: 0.299

Gnomad FIN AF: 0.236

Gnomad MID AF: 0.0791

Gnomad NFE AF: 0.168

Gnomad OTH AF: 0.226

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

GnomAD4 genome AF: 0.256 AC: 38772 AN: 151652 Hom.: 5898 Cov.: 30 AF XY: 0.260 AC XY: 19277 AN XY: 74104

African (AFR) AF: 0.413 AC: 17050 AN: 41326

American (AMR) AF: 0.228 AC: 3481 AN: 15242

Ashkenazi Jewish (ASJ) AF: 0.108 AC: 376 AN: 3466

East Asian (EAS) AF: 0.364 AC: 1880 AN: 5166

South Asian (SAS) AF: 0.301 AC: 1447 AN: 4812

European-Finnish (FIN) AF: 0.236 AC: 2454 AN: 10394

Middle Eastern (MID) AF: 0.0850 AC: 25 AN: 294

European-Non Finnish (NFE) AF: 0.168 AC: 11443 AN: 67938

Other (OTH) AF: 0.223 AC: 470 AN: 2104

Alfa AF: 0.184 Hom.: 3768

Bravo AF: 0.263

Asia WGS AF: 0.318 AC: 1103 AN: 3470

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	2.8
DANN	Benign	0.28
PhyloP100		-0.58

Splicing

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

Other links and lift over

dbSNP: rs9380006; hg19: chr6-27656499;