12-17567834-G-T

Variant names:

• chr12-17567834-G-T
• rs1163763
• ENST00000540399.1:n.763+13985C>A

Variant summary

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

The ENST00000540399.1(LINC02378):​n.763+13985C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.235 in 151,604 control chromosomes in the GnomAD database, including 4,363 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 0.23 (4363 hom., cov: 30)
• Consequence: LINC02378 ENST00000540399.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.24
• Publications: 2 publications found

Genes affected

LINC02378 (HGNC:53301): (long intergenic non-protein coding RNA 2378)

ENSG00000256389 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.255 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
LINC02378	ENST00000540399.1	n.763+13985C>A		intron_variant	Intron 6 of 7	5
LINC02378	ENST00000657845.1	n.451+13985C>A		intron_variant	Intron 5 of 6
ENSG00000256389	ENST00000669683.1	n.965+62782G>T		intron_variant	Intron 2 of 2

Frequencies

GnomAD3 genomes AF: 0.235 AC: 35595 AN: 151492 Hom.: 4365 Cov.: 30

Gnomad AFR AF: 0.218

Gnomad AMI AF: 0.388

Gnomad AMR AF: 0.190

Gnomad ASJ AF: 0.423

Gnomad EAS AF: 0.143

Gnomad SAS AF: 0.205

Gnomad FIN AF: 0.194

Gnomad MID AF: 0.309

Gnomad NFE AF: 0.258

Gnomad OTH AF: 0.262

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

GnomAD4 genome AF: 0.235 AC: 35607 AN: 151604 Hom.: 4363 Cov.: 30 AF XY: 0.230 AC XY: 17044 AN XY: 74068

African (AFR) AF: 0.218 AC: 9001 AN: 41376

American (AMR) AF: 0.190 AC: 2884 AN: 15210

Ashkenazi Jewish (ASJ) AF: 0.423 AC: 1464 AN: 3462

East Asian (EAS) AF: 0.142 AC: 731 AN: 5152

South Asian (SAS) AF: 0.206 AC: 988 AN: 4806

European-Finnish (FIN) AF: 0.194 AC: 2030 AN: 10476

Middle Eastern (MID) AF: 0.315 AC: 92 AN: 292

European-Non Finnish (NFE) AF: 0.258 AC: 17517 AN: 67818

Other (OTH) AF: 0.260 AC: 547 AN: 2102

Alfa AF: 0.0237 Hom.: 27

Bravo AF: 0.235

Asia WGS AF: 0.181 AC: 630 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	0.64
DANN	Benign	0.13
PhyloP100		-1.2

Splicing

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

Other links and lift over

dbSNP: rs1163763; hg19: chr12-17720768;