rs1940356

Positions:

• chr11-128209806-C-G

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NR_146647.1(LINC02098):​n.177+864C>G variant causes a intron, non coding transcript 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 NR_146647.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.677

Genes affected

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

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	UniProt
LINC02098	NR_146647.1	n.177+864C>G		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
LINC02098	ENST00000650607.1	n.195-731C>G		intron_variant, non_coding_transcript_variant
LINC02098	ENST00000608492.5	n.114+864C>G		intron_variant, non_coding_transcript_variant		3
LINC02098	ENST00000609260.2	n.163+864C>G		intron_variant, non_coding_transcript_variant		3
LINC02098	ENST00000667926.1	n.159+864C>G		intron_variant, non_coding_transcript_variant

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

Gnomad4 AFR AF: 0.0920

Gnomad4 AMR AF: 0.0578

Gnomad4 ASJ AF: 0.0657

Gnomad4 EAS AF: 0.141

Gnomad4 SAS AF: 0.0914

Gnomad4 FIN AF: 0.0786

Gnomad4 NFE AF: 0.0491

Gnomad4 OTH AF: 0.0555

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1940356; hg19: chr11-128079701;