chr3-55231293-C-T

Position:

• chr3-55231293-C-T

Variant summary

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

The NR_183740.1(LINC02030):​n.352+436C>T 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 0.318 in 151,998 control chromosomes in the GnomAD database, including 7,846 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 0.32 (7846 hom., cov: 32)
• Consequence: LINC02030 NR_183740.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.460

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=-1.03).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.358 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LINC02030	NR_183740.1	n.352+436C>T		intron_variant, non_coding_transcript_variant
LOC124906243	XR_007095917.1	n.158+35569G>A		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
LINC02030	ENST00000654581.1	n.202+440C>T		intron_variant, non_coding_transcript_variant
LINC02030	ENST00000662390.1	n.160+436C>T		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.318 AC: 48309 AN: 151880 Hom.: 7835 Cov.: 32

Gnomad AFR AF: 0.296

Gnomad AMI AF: 0.229

Gnomad AMR AF: 0.366

Gnomad ASJ AF: 0.334

Gnomad EAS AF: 0.176

Gnomad SAS AF: 0.179

Gnomad FIN AF: 0.325

Gnomad MID AF: 0.296

Gnomad NFE AF: 0.340

Gnomad OTH AF: 0.321

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

GnomAD4 genome AF: 0.318 AC: 48353 AN: 151998 Hom.: 7846 Cov.: 32 AF XY: 0.315 AC XY: 23384 AN XY: 74266

Gnomad4 AFR AF: 0.296

Gnomad4 AMR AF: 0.366

Gnomad4 ASJ AF: 0.334

Gnomad4 EAS AF: 0.176

Gnomad4 SAS AF: 0.179

Gnomad4 FIN AF: 0.325

Gnomad4 NFE AF: 0.340

Gnomad4 OTH AF: 0.324

Alfa AF: 0.334 Hom.: 12202

Bravo AF: 0.321

Asia WGS AF: 0.198 AC: 687 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.79
DANN	Benign	0.46

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6801136; hg19: chr3-55265321;