rs1490046

Variant names:

• chr5-174529044-G-A
• rs1490046
• ENST00000507361.5:n.1160G>A

Variant summary

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

The ENST00000507361.5(LINC01411):​n.1160G>A variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0784 in 152,170 control chromosomes in the GnomAD database, including 481 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 0.078 (481 hom., cov: 31)
  • Exomes 𝑓: 0.056 (0 hom.)
• Consequence: LINC01411 ENST00000507361.5 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0740
• Publications: 3 publications found

Genes affected

LINC01411 (HGNC:50703): (long intergenic non-protein coding RNA 1411)

LOC105377739 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.0855 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105377739	XR_941261.3	n.228-4354C>T		intron_variant	Intron 2 of 3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC01411	ENST00000507361.5	n.1160G>A		non_coding_transcript_exon_variant	Exon 4 of 4	3
LINC01411	ENST00000757676.1	n.1755G>A		non_coding_transcript_exon_variant	Exon 7 of 7
LINC01411	ENST00000504512.6	n.984+505G>A		intron_variant	Intron 5 of 6	3

Frequencies

GnomAD3 genomes AF: 0.0785 AC: 11937 AN: 152034 Hom.: 482 Cov.: 31

Gnomad AFR AF: 0.0880

Gnomad AMI AF: 0.00658

Gnomad AMR AF: 0.0559

Gnomad ASJ AF: 0.0302

Gnomad EAS AF: 0.0135

Gnomad SAS AF: 0.0882

Gnomad FIN AF: 0.115

Gnomad MID AF: 0.0411

Gnomad NFE AF: 0.0801

Gnomad OTH AF: 0.0737

GnomAD4 exome AF: 0.0556 AC: 1 AN: 18 Hom.: 0 Cov.: 0 AF XY: 0.100 AC XY: 1 AN XY: 10

⚠️ The allele balance in gnomAD version 4 Exomes is significantly skewed from the expected value of 0.5.

African (AFR) AC: 0 AN: 0

American (AMR) AC: 0 AN: 0

Ashkenazi Jewish (ASJ) AC: 0 AN: 0

East Asian (EAS) AC: 0 AN: 0

South Asian (SAS) AC: 0 AN: 0

European-Finnish (FIN) AC: 0 AN: 0

Middle Eastern (MID) AC: 0 AN: 0

European-Non Finnish (NFE) AF: 0.0556 AC: 1 AN: 18

Other (OTH) AC: 0 AN: 0

⚠️ The allele balance in gnomAD4 Exomes is highly skewed from 0.5 (p-value = 0), which strongly suggests a high chance of mosaicism in these individuals.

GnomAD4 genome AF: 0.0784 AC: 11934 AN: 152152 Hom.: 481 Cov.: 31 AF XY: 0.0786 AC XY: 5843 AN XY: 74380

African (AFR) AF: 0.0878 AC: 3647 AN: 41520

American (AMR) AF: 0.0557 AC: 852 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.0302 AC: 105 AN: 3472

East Asian (EAS) AF: 0.0133 AC: 69 AN: 5174

South Asian (SAS) AF: 0.0883 AC: 425 AN: 4812

European-Finnish (FIN) AF: 0.115 AC: 1221 AN: 10580

Middle Eastern (MID) AF: 0.0306 AC: 9 AN: 294

European-Non Finnish (NFE) AF: 0.0801 AC: 5446 AN: 67986

Other (OTH) AF: 0.0729 AC: 154 AN: 2112

Alfa AF: 0.0747 Hom.: 1308

Bravo AF: 0.0723

Asia WGS AF: 0.0860 AC: 299 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	8.9
DANN	Benign	0.81
PhyloP100		0.074
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: rs1490046; hg19: chr5-173956047;