6-33850152-T-C

Variant names:

• chr6-33850152-T-C
• rs4713693
• ENST00000799603.1:n.519-14721A>G

Variant summary

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

The ENST00000799603.1(LINC01016):​n.519-14721A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.45 in 151,996 control chromosomes in the GnomAD database, including 15,792 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 0.45 (15792 hom., cov: 32)
• Consequence: LINC01016 ENST00000799603.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.953
• Publications: 30 publications found

Genes affected

LINC01016 (HGNC:48991): (long intergenic non-protein coding RNA 1016)

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.508 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
LINC01016	ENST00000799603.1	n.519-14721A>G		intron_variant	Intron 2 of 2

Frequencies

GnomAD3 genomes AF: 0.450 AC: 68347 AN: 151878 Hom.: 15773 Cov.: 32

Gnomad AFR AF: 0.514

Gnomad AMI AF: 0.341

Gnomad AMR AF: 0.399

Gnomad ASJ AF: 0.486

Gnomad EAS AF: 0.260

Gnomad SAS AF: 0.311

Gnomad FIN AF: 0.493

Gnomad MID AF: 0.522

Gnomad NFE AF: 0.439

Gnomad OTH AF: 0.484

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

GnomAD4 genome AF: 0.450 AC: 68413 AN: 151996 Hom.: 15792 Cov.: 32 AF XY: 0.450 AC XY: 33412 AN XY: 74308

African (AFR) AF: 0.514 AC: 21293 AN: 41420

American (AMR) AF: 0.399 AC: 6101 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.486 AC: 1683 AN: 3466

East Asian (EAS) AF: 0.260 AC: 1346 AN: 5174

South Asian (SAS) AF: 0.311 AC: 1498 AN: 4824

European-Finnish (FIN) AF: 0.493 AC: 5199 AN: 10552

Middle Eastern (MID) AF: 0.531 AC: 155 AN: 292

European-Non Finnish (NFE) AF: 0.439 AC: 29807 AN: 67956

Other (OTH) AF: 0.484 AC: 1021 AN: 2108

Alfa AF: 0.440 Hom.: 69382

Bravo AF: 0.448

Asia WGS AF: 0.343 AC: 1191 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	15
DANN	Benign	0.80
PhyloP100		0.95

Splicing

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

Other links and lift over

dbSNP: rs4713693; hg19: chr6-33817929;