rs4085649

Variant names:

• chr1-83159053-G-T
• rs4085649
• ENST00000452901.5:n.1540-1553G>T

Variant summary

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

The ENST00000452901.5(LINC01362):​n.1540-1553G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.237 in 151,370 control chromosomes in the GnomAD database, including 4,911 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 0.24 (4911 hom., cov: 29)
• Consequence: LINC01362 ENST00000452901.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -3.69
• Publications: 1 publications found

Genes affected

LINC01362 (HGNC:50596): (long intergenic non-protein coding RNA 1362)

LINC01725 (HGNC:52513): (long intergenic non-protein coding RNA 1725)

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.299 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LINC01362	NR_147074.1	n.1540-1553G>T		intron_variant	Intron 9 of 10

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC01362	ENST00000452901.5	n.1540-1553G>T		intron_variant	Intron 9 of 10	1
LINC01725	ENST00000715939.1	n.272-56049C>A		intron_variant	Intron 3 of 4
LINC01725	ENST00000715963.1	n.398+23117C>A		intron_variant	Intron 1 of 2

Frequencies

GnomAD3 genomes AF: 0.237 AC: 35828 AN: 151250 Hom.: 4911 Cov.: 29

Gnomad AFR AF: 0.104

Gnomad AMI AF: 0.280

Gnomad AMR AF: 0.257

Gnomad ASJ AF: 0.330

Gnomad EAS AF: 0.263

Gnomad SAS AF: 0.247

Gnomad FIN AF: 0.250

Gnomad MID AF: 0.309

Gnomad NFE AF: 0.302

Gnomad OTH AF: 0.259

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

GnomAD4 genome AF: 0.237 AC: 35819 AN: 151370 Hom.: 4911 Cov.: 29 AF XY: 0.234 AC XY: 17277 AN XY: 73924

African (AFR) AF: 0.104 AC: 4282 AN: 41306

American (AMR) AF: 0.257 AC: 3895 AN: 15166

Ashkenazi Jewish (ASJ) AF: 0.330 AC: 1140 AN: 3456

East Asian (EAS) AF: 0.263 AC: 1348 AN: 5122

South Asian (SAS) AF: 0.248 AC: 1189 AN: 4794

European-Finnish (FIN) AF: 0.250 AC: 2607 AN: 10434

Middle Eastern (MID) AF: 0.301 AC: 88 AN: 292

European-Non Finnish (NFE) AF: 0.302 AC: 20481 AN: 67796

Other (OTH) AF: 0.255 AC: 535 AN: 2098

Alfa AF: 0.248 Hom.: 632

Bravo AF: 0.236

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	0.040
DANN	Benign	0.71
PhyloP100		-3.7
Mutation Taster		=100/0	polymorphism

Splicing

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

Other links and lift over

dbSNP: rs4085649; hg19: chr1-83624736;