rs1388875

Variant names:

• chr4-11754562-C-G
• rs1388875
• ENST00000506195.1:n.167-7510G>C

Variant summary

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

The ENST00000506195.1(LINC02360):​n.167-7510G>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.697 in 151,724 control chromosomes in the GnomAD database, including 36,902 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 0.70 (36902 hom., cov: 30)
• Consequence: LINC02360 ENST00000506195.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.919
• Publications: 0 publications found

Genes affected

LINC02360 (HGNC:53282): (long intergenic non-protein coding RNA 2360)

ENSG00000249631 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.708 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LINC02360	NR_146995.1	n.167-7510G>C		intron_variant	Intron 1 of 3
LOC107986178	NR_188483.1	n.268-15747C>G		intron_variant	Intron 2 of 4
LOC107986178	NR_188484.1	n.157-14166C>G		intron_variant	Intron 1 of 4
LOC107986178	NR_188485.1	n.157-15747C>G		intron_variant	Intron 1 of 3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC02360	ENST00000506195.1	n.167-7510G>C		intron_variant	Intron 1 of 3	3
ENSG00000249631	ENST00000508998.5	n.180-14166C>G		intron_variant	Intron 1 of 3	3
ENSG00000249631	ENST00000509244.3	n.153-15747C>G		intron_variant	Intron 1 of 3	5

Frequencies

GnomAD3 genomes AF: 0.697 AC: 105603 AN: 151606 Hom.: 36869 Cov.: 30

Gnomad AFR AF: 0.706

Gnomad AMI AF: 0.517

Gnomad AMR AF: 0.630

Gnomad ASJ AF: 0.743

Gnomad EAS AF: 0.642

Gnomad SAS AF: 0.694

Gnomad FIN AF: 0.677

Gnomad MID AF: 0.739

Gnomad NFE AF: 0.713

Gnomad OTH AF: 0.699

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

GnomAD4 genome AF: 0.697 AC: 105699 AN: 151724 Hom.: 36902 Cov.: 30 AF XY: 0.693 AC XY: 51394 AN XY: 74150

African (AFR) AF: 0.706 AC: 29185 AN: 41350

American (AMR) AF: 0.630 AC: 9607 AN: 15252

Ashkenazi Jewish (ASJ) AF: 0.743 AC: 2576 AN: 3468

East Asian (EAS) AF: 0.643 AC: 3305 AN: 5138

South Asian (SAS) AF: 0.697 AC: 3353 AN: 4814

European-Finnish (FIN) AF: 0.677 AC: 7106 AN: 10498

Middle Eastern (MID) AF: 0.729 AC: 213 AN: 292

European-Non Finnish (NFE) AF: 0.713 AC: 48423 AN: 67902

Other (OTH) AF: 0.696 AC: 1462 AN: 2102

Alfa AF: 0.694 Hom.: 4584

Bravo AF: 0.692

Asia WGS AF: 0.677 AC: 2351 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	1.3
DANN	Benign	0.56
PhyloP100		-0.92

Splicing

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

Other links and lift over

dbSNP: rs1388875; hg19: chr4-11756186;