chr5-174529044-G-A

Position:

• chr5-174529044-G-A

Variant summary

Our verdict is Benign. Variant got -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

Genes affected

LINC01411 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	Protein	UniProt
LOC105377739	XR_941261.3	n.228-4354C>T		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
LINC01411	ENST00000507361.5	n.1160G>A		non_coding_transcript_exon_variant	4/4	3
LINC01411	ENST00000506862.1	n.248-2286G>A		intron_variant		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

Gnomad4 NFE exome AF: 0.0556

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

Gnomad4 AFR AF: 0.0878

Gnomad4 AMR AF: 0.0557

Gnomad4 ASJ AF: 0.0302

Gnomad4 EAS AF: 0.0133

Gnomad4 SAS AF: 0.0883

Gnomad4 FIN AF: 0.115

Gnomad4 NFE AF: 0.0801

Gnomad4 OTH AF: 0.0729

Alfa AF: 0.0724 Hom.: 569

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1490046; hg19: chr5-173956047;