3-55197300-C-T

Variant names:

• chr3-55197300-C-T
• rs7620394
• ENST00000809726.1:n.284+7686C>T

Variant summary

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

The ENST00000809726.1(LINC02030):​n.284+7686C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.681 in 151,872 control chromosomes in the GnomAD database, including 35,697 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 0.68 (35697 hom., cov: 30)
• Consequence: LINC02030 ENST00000809726.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.465
• Publications: 2 publications found

Genes affected

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

LOC124906243 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -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 = 0.795 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000809726.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC02030	ENST00000809726.1		n.284+7686C>T		intron	N/A
	LINC02030	ENST00000809728.1		n.187-4496C>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.682 AC: 103440 AN: 151754 Hom.: 35684 Cov.: 30

Gnomad AFR AF: 0.569

Gnomad AMI AF: 0.718

Gnomad AMR AF: 0.686

Gnomad ASJ AF: 0.723

Gnomad EAS AF: 0.708

Gnomad SAS AF: 0.818

Gnomad FIN AF: 0.741

Gnomad MID AF: 0.729

Gnomad NFE AF: 0.725

Gnomad OTH AF: 0.680

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

GnomAD4 genome AF: 0.681 AC: 103493 AN: 151872 Hom.: 35697 Cov.: 30 AF XY: 0.686 AC XY: 50952 AN XY: 74230

African (AFR) AF: 0.569 AC: 23539 AN: 41396

American (AMR) AF: 0.686 AC: 10469 AN: 15260

Ashkenazi Jewish (ASJ) AF: 0.723 AC: 2509 AN: 3468

East Asian (EAS) AF: 0.709 AC: 3639 AN: 5136

South Asian (SAS) AF: 0.817 AC: 3924 AN: 4804

European-Finnish (FIN) AF: 0.741 AC: 7804 AN: 10530

Middle Eastern (MID) AF: 0.747 AC: 218 AN: 292

European-Non Finnish (NFE) AF: 0.725 AC: 49296 AN: 67966

Other (OTH) AF: 0.683 AC: 1440 AN: 2108

Alfa AF: 0.687 Hom.: 6349

Bravo AF: 0.665

Asia WGS AF: 0.753 AC: 2620 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	8.2
DANN	Benign	0.66
PhyloP100		0.47

Splicing

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

Other links and lift over

dbSNP: rs7620394; hg19: chr3-55231328;