1-73349948-T-G

Variant names:

• chr1-73349948-T-G
• rs10493515
• ENST00000415686.7:n.269-5125T>G

Variant summary

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

The ENST00000415686.7(LINC01360):​n.269-5125T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.458 in 151,442 control chromosomes in the GnomAD database, including 16,426 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 0.46 (16426 hom., cov: 30)
• Consequence: LINC01360 ENST00000415686.7 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.616
• Publications: 3 publications found

Genes affected

LINC01360 (HGNC:50593): (long intergenic non-protein coding RNA 1360)

ENSG00000295376 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.75 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
LINC01360	ENST00000415686.7	n.269-5125T>G		intron_variant	Intron 2 of 2	2
LINC01360	ENST00000635317.1	n.314-5125T>G		intron_variant	Intron 2 of 2	5
LINC01360	ENST00000657455.1	n.428-5125T>G		intron_variant	Intron 3 of 3

Frequencies

GnomAD3 genomes AF: 0.458 AC: 69350 AN: 151324 Hom.: 16428 Cov.: 30

Gnomad AFR AF: 0.389

Gnomad AMI AF: 0.529

Gnomad AMR AF: 0.371

Gnomad ASJ AF: 0.487

Gnomad EAS AF: 0.770

Gnomad SAS AF: 0.554

Gnomad FIN AF: 0.481

Gnomad MID AF: 0.503

Gnomad NFE AF: 0.484

Gnomad OTH AF: 0.447

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

GnomAD4 genome AF: 0.458 AC: 69368 AN: 151442 Hom.: 16426 Cov.: 30 AF XY: 0.460 AC XY: 34051 AN XY: 74000

African (AFR) AF: 0.388 AC: 16060 AN: 41386

American (AMR) AF: 0.371 AC: 5632 AN: 15178

Ashkenazi Jewish (ASJ) AF: 0.487 AC: 1680 AN: 3450

East Asian (EAS) AF: 0.770 AC: 3951 AN: 5134

South Asian (SAS) AF: 0.553 AC: 2659 AN: 4812

European-Finnish (FIN) AF: 0.481 AC: 5058 AN: 10526

Middle Eastern (MID) AF: 0.507 AC: 147 AN: 290

European-Non Finnish (NFE) AF: 0.484 AC: 32753 AN: 67652

Other (OTH) AF: 0.450 AC: 948 AN: 2106

Alfa AF: 0.466 Hom.: 2214

Bravo AF: 0.445

Asia WGS AF: 0.612 AC: 2123 AN: 3470

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	7.4
DANN	Benign	0.55
PhyloP100		0.62

Splicing

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

Other links and lift over

dbSNP: rs10493515; hg19: chr1-73815631;