rs416350

Variant names:

• chr12-68385633-G-A
• rs416350
• ENST00000441255.7:n.308-2031C>T

Your query was ambiguous. Multiple possible variants found:

• chr12-68385633-G-A
• chr12-68385633-G-C
• chr12-68385633-G-T

Variant summary

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

The ENST00000441255.7(LINC02384):​n.308-2031C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.057 in 152,052 control chromosomes in the GnomAD database, including 293 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 0.057 (293 hom., cov: 32)
• Consequence: LINC02384 ENST00000441255.7 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.472
• Publications: 8 publications found

Genes affected

LINC02384 (HGNC:53308): (long intergenic non-protein coding RNA 2384)

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.0737 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC02384	ENST00000441255.7	n.308-2031C>T		intron_variant	Intron 3 of 3	4
LINC02384	ENST00000539404.1	n.68+18100C>T		intron_variant	Intron 1 of 1	3
LINC02384	ENST00000546086.1	n.154-51969C>T		intron_variant	Intron 1 of 1	3

Frequencies

GnomAD3 genomes AF: 0.0570 AC: 8662 AN: 151934 Hom.: 293 Cov.: 32

Gnomad AFR AF: 0.0759

Gnomad AMI AF: 0.0385

Gnomad AMR AF: 0.0284

Gnomad ASJ AF: 0.0314

Gnomad EAS AF: 0.0235

Gnomad SAS AF: 0.0351

Gnomad FIN AF: 0.0548

Gnomad MID AF: 0.0285

Gnomad NFE AF: 0.0583

Gnomad OTH AF: 0.0488

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

GnomAD4 genome AF: 0.0570 AC: 8667 AN: 152052 Hom.: 293 Cov.: 32 AF XY: 0.0559 AC XY: 4155 AN XY: 74336

African (AFR) AF: 0.0759 AC: 3144 AN: 41440

American (AMR) AF: 0.0284 AC: 434 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.0314 AC: 109 AN: 3468

East Asian (EAS) AF: 0.0237 AC: 123 AN: 5188

South Asian (SAS) AF: 0.0351 AC: 169 AN: 4812

European-Finnish (FIN) AF: 0.0548 AC: 579 AN: 10566

Middle Eastern (MID) AF: 0.0306 AC: 9 AN: 294

European-Non Finnish (NFE) AF: 0.0583 AC: 3963 AN: 67982

Other (OTH) AF: 0.0482 AC: 102 AN: 2114

Alfa AF: 0.0540 Hom.: 992

Bravo AF: 0.0534

Asia WGS AF: 0.0410 AC: 143 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	1.6
DANN	Benign	0.70
PhyloP100		-0.47
Mutation Taster		=100/0	polymorphism (auto)

Splicing

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

Other links and lift over

dbSNP: rs416350; hg19: chr12-68779413;