chr3-55203710-C-T

Variant names:

• chr3-55203710-C-T
• rs10510777
• ENST00000809726.1:n.284+14096C>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+14096C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.447 in 152,084 control chromosomes in the GnomAD database, including 16,087 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 0.45 (16087 hom., cov: 32)
• Consequence: LINC02030 ENST00000809726.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 2.07
• 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 (EAS) allele frequency at 95% confidence interval = 0.683 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC124906243	XR_007095917.1	n.159-59788G>A		intron_variant	Intron 2 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC02030	ENST00000809726.1	n.284+14096C>T		intron_variant	Intron 1 of 2

Frequencies

GnomAD3 genomes AF: 0.448 AC: 68020 AN: 151966 Hom.: 16078 Cov.: 32

Gnomad AFR AF: 0.317

Gnomad AMI AF: 0.627

Gnomad AMR AF: 0.458

Gnomad ASJ AF: 0.520

Gnomad EAS AF: 0.701

Gnomad SAS AF: 0.693

Gnomad FIN AF: 0.501

Gnomad MID AF: 0.411

Gnomad NFE AF: 0.474

Gnomad OTH AF: 0.443

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

GnomAD4 genome AF: 0.447 AC: 68049 AN: 152084 Hom.: 16087 Cov.: 32 AF XY: 0.456 AC XY: 33857 AN XY: 74308

African (AFR) AF: 0.317 AC: 13147 AN: 41492

American (AMR) AF: 0.458 AC: 6995 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.520 AC: 1806 AN: 3472

East Asian (EAS) AF: 0.702 AC: 3623 AN: 5164

South Asian (SAS) AF: 0.693 AC: 3338 AN: 4818

European-Finnish (FIN) AF: 0.501 AC: 5293 AN: 10570

Middle Eastern (MID) AF: 0.418 AC: 123 AN: 294

European-Non Finnish (NFE) AF: 0.474 AC: 32205 AN: 67978

Other (OTH) AF: 0.449 AC: 947 AN: 2110

Alfa AF: 0.449 Hom.: 18936

Bravo AF: 0.434

Asia WGS AF: 0.676 AC: 2349 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	6.9
DANN	Benign	0.71
PhyloP100		2.1

Splicing

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

Other links and lift over

dbSNP: rs10510777; hg19: chr3-55237738;