ENST00000435973.3:n.401-848T>G

Variant names:

• chr1-229876569-A-C
• rs12070887
• ENST00000435973.3:n.401-848T>G

Variant summary

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

The ENST00000435973.3(LINC01682):​n.401-848T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.201 in 152,182 control chromosomes in the GnomAD database, including 10,181 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 0.20 (10181 hom., cov: 32)
• Consequence: LINC01682 ENST00000435973.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.650
• Publications: 4 publications found

Genes affected

LINC01682 (HGNC:52470): (long intergenic non-protein coding RNA 1682)

ENSG00000304899 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.685 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LINC01682	NR_146476.1	n.280-848T>G		intron_variant	Intron 1 of 1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC01682	ENST00000435973.3	n.401-848T>G		intron_variant	Intron 2 of 2	2
LINC01682	ENST00000650825.1	n.44-848T>G		intron_variant	Intron 1 of 8
LINC01682	ENST00000661713.1	n.336-848T>G		intron_variant	Intron 2 of 6

Frequencies

GnomAD3 genomes AF: 0.201 AC: 30574 AN: 152064 Hom.: 10155 Cov.: 32

Gnomad AFR AF: 0.692

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0816

Gnomad ASJ AF: 0.0110

Gnomad EAS AF: 0.000193

Gnomad SAS AF: 0.00849

Gnomad FIN AF: 0.000188

Gnomad MID AF: 0.0854

Gnomad NFE AF: 0.00448

Gnomad OTH AF: 0.149

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

GnomAD4 genome AF: 0.201 AC: 30646 AN: 152182 Hom.: 10181 Cov.: 32 AF XY: 0.194 AC XY: 14448 AN XY: 74420

African (AFR) AF: 0.692 AC: 28680 AN: 41448

American (AMR) AF: 0.0814 AC: 1245 AN: 15298

Ashkenazi Jewish (ASJ) AF: 0.0110 AC: 38 AN: 3470

East Asian (EAS) AF: 0.000193 AC: 1 AN: 5182

South Asian (SAS) AF: 0.00767 AC: 37 AN: 4824

European-Finnish (FIN) AF: 0.000188 AC: 2 AN: 10620

Middle Eastern (MID) AF: 0.0884 AC: 26 AN: 294

European-Non Finnish (NFE) AF: 0.00447 AC: 304 AN: 68018

Other (OTH) AF: 0.148 AC: 313 AN: 2116

Alfa AF: 0.135 Hom.: 2553

Bravo AF: 0.231

Asia WGS AF: 0.0520 AC: 183 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	3.0
DANN	Benign	0.82
PhyloP100		-0.65
Mutation Taster		=100/0	polymorphism

Splicing

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

Other links and lift over

dbSNP: rs12070887; hg19: chr1-230012316;