chr3-55237208-C-T

Position:

• chr3-55237208-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+6351C>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 0.273 in 152,028 control chromosomes in the GnomAD database, including 5,868 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 0.27 (5868 hom., cov: 32)
• Consequence: LINC02030 NR_183740.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.132

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=-0.84).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.305 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LINC02030	NR_183740.1	n.352+6351C>T		intron_variant, non_coding_transcript_variant
LOC124906243	XR_007095917.1	n.158+29654G>A		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
LINC02030	ENST00000654581.1	n.362+3849C>T		intron_variant, non_coding_transcript_variant
LINC02030	ENST00000662390.1	n.320+3849C>T		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.273 AC: 41458 AN: 151910 Hom.: 5869 Cov.: 32

Gnomad AFR AF: 0.241

Gnomad AMI AF: 0.232

Gnomad AMR AF: 0.269

Gnomad ASJ AF: 0.312

Gnomad EAS AF: 0.0944

Gnomad SAS AF: 0.277

Gnomad FIN AF: 0.246

Gnomad MID AF: 0.342

Gnomad NFE AF: 0.309

Gnomad OTH AF: 0.286

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

GnomAD4 genome AF: 0.273 AC: 41483 AN: 152028 Hom.: 5868 Cov.: 32 AF XY: 0.267 AC XY: 19831 AN XY: 74302

Gnomad4 AFR AF: 0.241

Gnomad4 AMR AF: 0.269

Gnomad4 ASJ AF: 0.312

Gnomad4 EAS AF: 0.0946

Gnomad4 SAS AF: 0.277

Gnomad4 FIN AF: 0.246

Gnomad4 NFE AF: 0.309

Gnomad4 OTH AF: 0.283

Alfa AF: 0.307 Hom.: 3977

Bravo AF: 0.273

Asia WGS AF: 0.173 AC: 601 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	3.0
DANN	Benign	0.72

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs920891; hg19: chr3-55271236;