3-84885341-G-T

Position:

• chr3-84885341-G-T

Variant summary

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

The ENST00000488348.1(LINC02025):​n.188+218G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.427 in 151,942 control chromosomes in the GnomAD database, including 14,441 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 0.43 (14441 hom., cov: 32)
• Consequence: LINC02025 ENST00000488348.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.926

Genes affected

LINC02025 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.564 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LINC02025	NR_147147.1	n.195+218G>T		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
LINC02025	ENST00000488348.1	n.188+218G>T		intron_variant		3
LINC02025	ENST00000661831.1	n.223+296G>T		intron_variant

Frequencies

GnomAD3 genomes AF: 0.427 AC: 64868 AN: 151822 Hom.: 14428 Cov.: 32

Gnomad AFR AF: 0.571

Gnomad AMI AF: 0.302

Gnomad AMR AF: 0.409

Gnomad ASJ AF: 0.349

Gnomad EAS AF: 0.440

Gnomad SAS AF: 0.374

Gnomad FIN AF: 0.487

Gnomad MID AF: 0.434

Gnomad NFE AF: 0.345

Gnomad OTH AF: 0.377

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

GnomAD4 genome AF: 0.427 AC: 64934 AN: 151942 Hom.: 14441 Cov.: 32 AF XY: 0.433 AC XY: 32165 AN XY: 74284

Gnomad4 AFR AF: 0.571

Gnomad4 AMR AF: 0.409

Gnomad4 ASJ AF: 0.349

Gnomad4 EAS AF: 0.440

Gnomad4 SAS AF: 0.372

Gnomad4 FIN AF: 0.487

Gnomad4 NFE AF: 0.345

Gnomad4 OTH AF: 0.378

Alfa AF: 0.395 Hom.: 1513

Bravo AF: 0.427

Asia WGS AF: 0.449 AC: 1566 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	1.2
DANN	Benign	0.23

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs649851; hg19: chr3-84934492;