rs1387395

Variant names:

• chr5-164474440-A-G
• rs1387395
• ENST00000486913.3:n.86-12229A>G

Variant summary

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

The ENST00000486913.3(LINC03000):​n.86-12229A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.764 in 152,154 control chromosomes in the GnomAD database, including 44,718 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 0.76 (44718 hom., cov: 32)
• Consequence: LINC03000 ENST00000486913.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.581
• Publications: 1 publications found

Genes affected

LINC03000 (HGNC:56116): (long intergenic non-protein coding RNA 3000)

LOC102546299 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.829 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC102546299	NR_105065.1	n.190+3972A>G		intron_variant	Intron 1 of 3
LINC03000	XR_001742489.2	n.576+120216A>G		intron_variant	Intron 2 of 4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC03000	ENST00000486913.3	n.86-12229A>G		intron_variant	Intron 1 of 2	2
LINC03000	ENST00000517508.5	n.586-12229A>G		intron_variant	Intron 2 of 5	4
LINC03000	ENST00000519327.5	n.390+5542A>G		intron_variant	Intron 3 of 4	3

Frequencies

GnomAD3 genomes AF: 0.763 AC: 116079 AN: 152036 Hom.: 44676 Cov.: 32

Gnomad AFR AF: 0.837

Gnomad AMI AF: 0.674

Gnomad AMR AF: 0.836

Gnomad ASJ AF: 0.800

Gnomad EAS AF: 0.616

Gnomad SAS AF: 0.821

Gnomad FIN AF: 0.684

Gnomad MID AF: 0.794

Gnomad NFE AF: 0.720

Gnomad OTH AF: 0.799

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

GnomAD4 genome AF: 0.764 AC: 116176 AN: 152154 Hom.: 44718 Cov.: 32 AF XY: 0.767 AC XY: 57019 AN XY: 74384

African (AFR) AF: 0.837 AC: 34736 AN: 41514

American (AMR) AF: 0.836 AC: 12778 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.800 AC: 2776 AN: 3472

East Asian (EAS) AF: 0.616 AC: 3182 AN: 5168

South Asian (SAS) AF: 0.820 AC: 3960 AN: 4828

European-Finnish (FIN) AF: 0.684 AC: 7231 AN: 10574

Middle Eastern (MID) AF: 0.803 AC: 236 AN: 294

European-Non Finnish (NFE) AF: 0.720 AC: 48975 AN: 67994

Other (OTH) AF: 0.798 AC: 1687 AN: 2114

Alfa AF: 0.751 Hom.: 73479

Bravo AF: 0.777

Asia WGS AF: 0.753 AC: 2623 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	2.7
DANN	Benign	0.79
PhyloP100		0.58

Splicing

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

Other links and lift over

dbSNP: rs1387395; hg19: chr5-163901446;