chr11-128210003-C-A

Variant names:

• chr11-128210003-C-A
• rs1940357
• ENST00000608492.5:n.114+1061C>A

Variant summary

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

The ENST00000608492.5(LINC02098):​n.114+1061C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0684 in 152,220 control chromosomes in the GnomAD database, including 429 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 0.068 (429 hom., cov: 33)
• Consequence: LINC02098 ENST00000608492.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.564
• Publications: 2 publications found

Genes affected

LINC02098 (HGNC:52950): (long intergenic non-protein coding RNA 2098)

ENSG00000301990 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.132 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LINC02098	NR_146647.1	n.177+1061C>A		intron_variant	Intron 1 of 3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC02098	ENST00000608492.5	n.114+1061C>A		intron_variant	Intron 1 of 3	3
LINC02098	ENST00000609260.2	n.163+1061C>A		intron_variant	Intron 1 of 3	3
LINC02098	ENST00000650607.2	n.195-534C>A		intron_variant	Intron 1 of 4

Frequencies

GnomAD3 genomes AF: 0.0684 AC: 10400 AN: 152102 Hom.: 435 Cov.: 33

Gnomad AFR AF: 0.0922

Gnomad AMI AF: 0.0175

Gnomad AMR AF: 0.0573

Gnomad ASJ AF: 0.0657

Gnomad EAS AF: 0.141

Gnomad SAS AF: 0.0901

Gnomad FIN AF: 0.0778

Gnomad MID AF: 0.0570

Gnomad NFE AF: 0.0491

Gnomad OTH AF: 0.0560

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

GnomAD4 genome AF: 0.0684 AC: 10408 AN: 152220 Hom.: 429 Cov.: 33 AF XY: 0.0704 AC XY: 5239 AN XY: 74418

African (AFR) AF: 0.0920 AC: 3820 AN: 41538

American (AMR) AF: 0.0576 AC: 881 AN: 15300

Ashkenazi Jewish (ASJ) AF: 0.0657 AC: 228 AN: 3472

East Asian (EAS) AF: 0.141 AC: 729 AN: 5182

South Asian (SAS) AF: 0.0912 AC: 440 AN: 4822

European-Finnish (FIN) AF: 0.0778 AC: 823 AN: 10576

Middle Eastern (MID) AF: 0.0408 AC: 12 AN: 294

European-Non Finnish (NFE) AF: 0.0491 AC: 3341 AN: 68012

Other (OTH) AF: 0.0559 AC: 118 AN: 2112

Alfa AF: 0.0521 Hom.: 740

Bravo AF: 0.0656

Asia WGS AF: 0.127 AC: 442 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	1.6
DANN	Benign	0.30
PhyloP100		0.56

Splicing

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

Other links and lift over

dbSNP: rs1940357; hg19: chr11-128079898;