rs1186300

Variant names:

• chr12-17576057-C-A
• rs1186300
• ENST00000540399.1:n.763+5762G>T

Your query was ambiguous. Multiple possible variants found:

• chr12-17576057-C-A
• chr12-17576057-C-G
• chr12-17576057-C-T

Variant summary

Our verdict is Likely benign. The variant received -6 ACMG points: 0P and 6B. BP4_Moderate BS2

The ENST00000540399.1(LINC02378):​n.763+5762G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00212 in 151,360 control chromosomes in the GnomAD database, including 2 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 0.0021 (2 hom., cov: 31)
• Consequence: LINC02378 ENST00000540399.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.569
• Publications: 4 publications found

Genes affected

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

ENSG00000256389 (HGNC:):

ACMG classification

Our verdict: Likely_benign. The variant received -6 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.28).
• BS2: High Homozygotes in GnomAd4 at 2 gene

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+5762G>T		intron_variant	Intron 6 of 7	5
LINC02378	ENST00000657845.1	n.451+5762G>T		intron_variant	Intron 5 of 6
ENSG00000256389	ENST00000669683.1	n.965+71005C>A		intron_variant	Intron 2 of 2

Frequencies

GnomAD3 genomes AF: 0.00212 AC: 321 AN: 151240 Hom.: 2 Cov.: 31

Gnomad AFR AF: 0.00748

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.000659

Gnomad ASJ AF: 0.00

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.000207

Gnomad FIN AF: 0.00

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.00

Gnomad OTH AF: 0.000959

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

GnomAD4 genome AF: 0.00212 AC: 321 AN: 151360 Hom.: 2 Cov.: 31 AF XY: 0.00207 AC XY: 153 AN XY: 73924

African (AFR) AF: 0.00749 AC: 309 AN: 41280

American (AMR) AF: 0.000658 AC: 10 AN: 15198

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 3458

East Asian (EAS) AF: 0.00 AC: 0 AN: 5114

South Asian (SAS) AF: 0.00 AC: 0 AN: 4832

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 10492

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 292

European-Non Finnish (NFE) AF: 0.00 AC: 0 AN: 67678

Other (OTH) AF: 0.000949 AC: 2 AN: 2108

Alfa AF: 0.00 Hom.: 57071

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.28
CADD	Benign	14
DANN	Benign	0.73
PhyloP100		0.57

Splicing

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

Other links and lift over

dbSNP: rs1186300; hg19: chr12-17728991;