17-48672429-A-C

Variant names:

• chr17-48672429-A-C
• rs8074700
• ENST00000575202.3:n.176-10810A>C

Variant summary

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

The NR_189644.1(LINC02086):​n.602-10830A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.68 in 152,086 control chromosomes in the GnomAD database, including 35,663 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 0.68 (35663 hom., cov: 32)
• Consequence: LINC02086 NR_189644.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0960
• Publications: 8 publications found

Genes affected

LINC02086 (HGNC:52936): (long intergenic non-protein coding RNA 2086)

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 (SAS) allele frequency at 95% confidence interval = 0.742 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NR_189644.1. 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
	LINC02086	NR_189644.1		n.602-10830A>C		intron	N/A
	LINC02086	NR_189645.1		n.3886-10830A>C		intron	N/A
	LINC02086	NR_189646.1		n.345+19455A>C		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC02086	ENST00000575202.3	TSL:5	n.176-10810A>C		intron	N/A
	LINC02086	ENST00000628006.2	TSL:5	n.182-10810A>C		intron	N/A
	LINC02086	ENST00000765376.1		n.226-10830A>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.680 AC: 103348 AN: 151968 Hom.: 35632 Cov.: 32

Gnomad AFR AF: 0.562

Gnomad AMI AF: 0.776

Gnomad AMR AF: 0.750

Gnomad ASJ AF: 0.726

Gnomad EAS AF: 0.583

Gnomad SAS AF: 0.764

Gnomad FIN AF: 0.617

Gnomad MID AF: 0.696

Gnomad NFE AF: 0.743

Gnomad OTH AF: 0.701

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

GnomAD4 genome AF: 0.680 AC: 103429 AN: 152086 Hom.: 35663 Cov.: 32 AF XY: 0.677 AC XY: 50313 AN XY: 74342

African (AFR) AF: 0.562 AC: 23286 AN: 41454

American (AMR) AF: 0.750 AC: 11467 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.726 AC: 2522 AN: 3472

East Asian (EAS) AF: 0.583 AC: 3020 AN: 5176

South Asian (SAS) AF: 0.763 AC: 3679 AN: 4822

European-Finnish (FIN) AF: 0.617 AC: 6526 AN: 10570

Middle Eastern (MID) AF: 0.704 AC: 207 AN: 294

European-Non Finnish (NFE) AF: 0.743 AC: 50531 AN: 67996

Other (OTH) AF: 0.704 AC: 1483 AN: 2108

Alfa AF: 0.705 Hom.: 38001

Bravo AF: 0.683

Asia WGS AF: 0.709 AC: 2468 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	4.4
DANN	Benign	0.69
PhyloP100		-0.096

Splicing

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

Other links and lift over

dbSNP: rs8074700; hg19: chr17-46749791;