rs358806

Positions:

• chr3-55279372-A-C
• chr3-55279372-A-G
• chr3-55279372-A-T

Variant summary

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

The NR_183740.1(LINC02030):​n.484-6946A>C 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 0.825 in 152,216 control chromosomes in the GnomAD database, including 52,099 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 0.82 (52099 hom., cov: 34)
• Consequence: LINC02030 NR_183740.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.129

Genes affected

LINC02030 (HGNC:52864): (long intergenic non-protein coding RNA 2030)

LOC124906243 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.89 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LINC02030	NR_183740.1	n.484-6946A>C		intron_variant, non_coding_transcript_variant
LOC124906243	XR_007095917.1	n.100-12452T>G		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
LINC02030	ENST00000654581.1	n.363-6946A>C		intron_variant, non_coding_transcript_variant
LINC02030	ENST00000662390.1	n.321-6946A>C		intron_variant, non_coding_transcript_variant
LINC02030	ENST00000670191.1	n.213-6946A>C		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.825 AC: 125446 AN: 152098 Hom.: 52051 Cov.: 34

Gnomad AFR AF: 0.889

Gnomad AMI AF: 0.787

Gnomad AMR AF: 0.811

Gnomad ASJ AF: 0.789

Gnomad EAS AF: 0.788

Gnomad SAS AF: 0.912

Gnomad FIN AF: 0.744

Gnomad MID AF: 0.886

Gnomad NFE AF: 0.801

Gnomad OTH AF: 0.806

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

GnomAD4 genome AF: 0.825 AC: 125550 AN: 152216 Hom.: 52099 Cov.: 34 AF XY: 0.824 AC XY: 61290 AN XY: 74404

Gnomad4 AFR AF: 0.889

Gnomad4 AMR AF: 0.810

Gnomad4 ASJ AF: 0.789

Gnomad4 EAS AF: 0.788

Gnomad4 SAS AF: 0.912

Gnomad4 FIN AF: 0.744

Gnomad4 NFE AF: 0.801

Gnomad4 OTH AF: 0.806

Alfa AF: 0.802 Hom.: 109248

Bravo AF: 0.828

Asia WGS AF: 0.863 AC: 3002 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.25
DANN	Benign	0.43

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs358806; hg19: chr3-55313400;