rs1388875

chr4-11754562-C-G

Variant summary

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

The NR_146995.1(LINC02360):n.167-7510G>C variant causes a intron, non coding transcript 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 NR_146995.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.919

Genes affected

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

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	UniProt
LINC02360	NR_146995.1	n.167-7510G>C		intron_variant, non_coding_transcript_variant
LOC107986178	XR_001741361.2	n.1743-8897C>G		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
LINC02360	ENST00000506195.1	n.167-7510G>C		intron_variant, non_coding_transcript_variant		3
	ENST00000510095.5	n.99-8897C>G		intron_variant, non_coding_transcript_variant		3

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

Gnomad4 AFR AF: 0.706

Gnomad4 AMR AF: 0.630

Gnomad4 ASJ AF: 0.743

Gnomad4 EAS AF: 0.643

Gnomad4 SAS AF: 0.697

Gnomad4 FIN AF: 0.677

Gnomad4 NFE AF: 0.713

Gnomad4 OTH AF: 0.696

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1388875; hg19: chr4-11756186;