rs1882646

Variant names:

• chr2-10891662-A-G
• rs1882646
• ENST00000743683.1:n.28-9554A>G

Variant summary

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

The ENST00000743683.1(LINC01954):​n.28-9554A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.299 in 152,162 control chromosomes in the GnomAD database, including 10,822 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 0.30 (10822 hom., cov: 32)
• Consequence: LINC01954 ENST00000743683.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.665
• Publications: 5 publications found

Genes affected

LINC01954 (HGNC:52779): (long intergenic non-protein coding RNA 1954)

ENSG00000296957 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.65).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.658 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
LINC01954	ENST00000743683.1	n.28-9554A>G		intron_variant	Intron 1 of 1
LINC01954	ENST00000743684.1	n.265-9554A>G		intron_variant	Intron 1 of 1
LINC01954	ENST00000743685.1	n.217-9554A>G		intron_variant	Intron 2 of 2
ENSG00000296957	ENST00000743884.1	n.54-1107T>C		intron_variant	Intron 1 of 2

Frequencies

GnomAD3 genomes AF: 0.299 AC: 45438 AN: 152044 Hom.: 10776 Cov.: 32

Gnomad AFR AF: 0.664

Gnomad AMI AF: 0.120

Gnomad AMR AF: 0.194

Gnomad ASJ AF: 0.186

Gnomad EAS AF: 0.171

Gnomad SAS AF: 0.186

Gnomad FIN AF: 0.144

Gnomad MID AF: 0.297

Gnomad NFE AF: 0.152

Gnomad OTH AF: 0.264

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

GnomAD4 genome AF: 0.299 AC: 45543 AN: 152162 Hom.: 10822 Cov.: 32 AF XY: 0.295 AC XY: 21931 AN XY: 74374

African (AFR) AF: 0.665 AC: 27573 AN: 41482

American (AMR) AF: 0.193 AC: 2957 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.186 AC: 647 AN: 3472

East Asian (EAS) AF: 0.170 AC: 881 AN: 5168

South Asian (SAS) AF: 0.187 AC: 901 AN: 4824

European-Finnish (FIN) AF: 0.144 AC: 1523 AN: 10610

Middle Eastern (MID) AF: 0.293 AC: 86 AN: 294

European-Non Finnish (NFE) AF: 0.152 AC: 10303 AN: 67992

Other (OTH) AF: 0.266 AC: 563 AN: 2114

Alfa AF: 0.200 Hom.: 14642

Bravo AF: 0.317

Asia WGS AF: 0.230 AC: 799 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.65
CADD	Benign	13
DANN	Benign	0.87
PhyloP100		-0.67

Splicing

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

Other links and lift over

dbSNP: rs1882646; hg19: chr2-11031788;