rs1940356

Variant names:

• chr11-128209806-C-G
• rs1940356
• ENST00000608492.5:n.114+864C>G

Variant summary

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

The ENST00000608492.5(LINC02098):​n.114+864C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0685 in 152,166 control chromosomes in the GnomAD database, including 432 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 (432 hom., cov: 33)
• Consequence: LINC02098 ENST00000608492.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.677
• Publications: 1 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=-0.86).
• 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+864C>G		intron_variant	Intron 1 of 3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC02098	ENST00000608492.5	n.114+864C>G		intron_variant	Intron 1 of 3	3
LINC02098	ENST00000609260.2	n.163+864C>G		intron_variant	Intron 1 of 3	3
LINC02098	ENST00000650607.2	n.195-731C>G		intron_variant	Intron 1 of 4

Frequencies

GnomAD3 genomes AF: 0.0685 AC: 10412 AN: 152048 Hom.: 438 Cov.: 33

Gnomad AFR AF: 0.0922

Gnomad AMI AF: 0.0175

Gnomad AMR AF: 0.0576

Gnomad ASJ AF: 0.0657

Gnomad EAS AF: 0.141

Gnomad SAS AF: 0.0902

Gnomad FIN AF: 0.0786

Gnomad MID AF: 0.0570

Gnomad NFE AF: 0.0491

Gnomad OTH AF: 0.0556

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

GnomAD4 genome AF: 0.0685 AC: 10420 AN: 152166 Hom.: 432 Cov.: 33 AF XY: 0.0707 AC XY: 5256 AN XY: 74386

African (AFR) AF: 0.0920 AC: 3821 AN: 41512

American (AMR) AF: 0.0578 AC: 884 AN: 15286

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

East Asian (EAS) AF: 0.141 AC: 729 AN: 5178

South Asian (SAS) AF: 0.0914 AC: 440 AN: 4816

European-Finnish (FIN) AF: 0.0786 AC: 832 AN: 10580

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

European-Non Finnish (NFE) AF: 0.0491 AC: 3341 AN: 68006

Other (OTH) AF: 0.0555 AC: 117 AN: 2110

Alfa AF: 0.0646 Hom.: 51

Bravo AF: 0.0656

Asia WGS AF: 0.126 AC: 440 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	0.43
DANN	Benign	0.32
PhyloP100		-0.68

Splicing

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

Other links and lift over

dbSNP: rs1940356; hg19: chr11-128079701;