rs2104362

Variant names:

• chr6-33857581-G-A
• rs2104362
• ENST00000799603.1:n.519-22150C>T

Variant summary

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

The ENST00000799603.1(LINC01016):​n.519-22150C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.69 in 152,022 control chromosomes in the GnomAD database, including 36,559 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 0.69 (36559 hom., cov: 31)
• Consequence: LINC01016 ENST00000799603.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0540
• Publications: 9 publications found

Genes affected

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

LOC105375027 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.727 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105375027	XR_007059554.1	n.236+1143G>A		intron_variant	Intron 1 of 4
LOC105375027	XR_007059555.1	n.237+1143G>A		intron_variant	Intron 1 of 3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC01016	ENST00000799603.1	n.519-22150C>T		intron_variant	Intron 2 of 2

Frequencies

GnomAD3 genomes AF: 0.690 AC: 104869 AN: 151904 Hom.: 36538 Cov.: 31

Gnomad AFR AF: 0.647

Gnomad AMI AF: 0.616

Gnomad AMR AF: 0.663

Gnomad ASJ AF: 0.677

Gnomad EAS AF: 0.466

Gnomad SAS AF: 0.655

Gnomad FIN AF: 0.758

Gnomad MID AF: 0.797

Gnomad NFE AF: 0.733

Gnomad OTH AF: 0.699

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

GnomAD4 genome AF: 0.690 AC: 104935 AN: 152022 Hom.: 36559 Cov.: 31 AF XY: 0.690 AC XY: 51290 AN XY: 74348

African (AFR) AF: 0.647 AC: 26794 AN: 41426

American (AMR) AF: 0.663 AC: 10131 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.677 AC: 2348 AN: 3470

East Asian (EAS) AF: 0.466 AC: 2396 AN: 5142

South Asian (SAS) AF: 0.656 AC: 3162 AN: 4820

European-Finnish (FIN) AF: 0.758 AC: 8035 AN: 10604

Middle Eastern (MID) AF: 0.796 AC: 234 AN: 294

European-Non Finnish (NFE) AF: 0.733 AC: 49806 AN: 67960

Other (OTH) AF: 0.696 AC: 1467 AN: 2108

Alfa AF: 0.716 Hom.: 77161

Bravo AF: 0.681

Asia WGS AF: 0.595 AC: 2069 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	1.4
DANN	Benign	0.53
PhyloP100		-0.054

Splicing

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

Other links and lift over

dbSNP: rs2104362; hg19: chr6-33825358; COSMIC: COSV66104041;