4-111841680-G-T

Variant names:

• chr4-111841680-G-T
• rs377426
• ENST00000511219.1:n.135-12630C>A

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000511219.1(LINC02945):​n.135-12630C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.551 in 151,558 control chromosomes in the GnomAD database, including 23,750 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 0.55 (23750 hom., cov: 32)
• Consequence: LINC02945 ENST00000511219.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.311

Genes affected

LINC02945 (HGNC:55960): (long intergenic non-protein coding RNA 2945)

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.01).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.613 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LINC02945	NR_186680.1	n.99-12630C>A		intron_variant	Intron 1 of 2
LINC02945	NR_186681.1	n.185-12630C>A		intron_variant	Intron 2 of 3
LINC02945	NR_186682.1	n.83-12630C>A		intron_variant	Intron 1 of 2
LINC02945	NR_186683.1	n.63-31964C>A		intron_variant	Intron 1 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC02945	ENST00000511219.1	n.135-12630C>A		intron_variant	Intron 1 of 2	3
LINC02945	ENST00000679735.1	n.188-12630C>A		intron_variant	Intron 2 of 3

Frequencies

GnomAD3 genomes AF: 0.551 AC: 83453 AN: 151440 Hom.: 23714 Cov.: 32

Gnomad AFR AF: 0.392

Gnomad AMI AF: 0.700

Gnomad AMR AF: 0.578

Gnomad ASJ AF: 0.632

Gnomad EAS AF: 0.540

Gnomad SAS AF: 0.503

Gnomad FIN AF: 0.689

Gnomad MID AF: 0.436

Gnomad NFE AF: 0.618

Gnomad OTH AF: 0.582

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

GnomAD4 genome AF: 0.551 AC: 83530 AN: 151558 Hom.: 23750 Cov.: 32 AF XY: 0.554 AC XY: 40982 AN XY: 74012

Gnomad4 AFR AF: 0.393

Gnomad4 AMR AF: 0.577

Gnomad4 ASJ AF: 0.632

Gnomad4 EAS AF: 0.540

Gnomad4 SAS AF: 0.503

Gnomad4 FIN AF: 0.689

Gnomad4 NFE AF: 0.618

Gnomad4 OTH AF: 0.588

Alfa AF: 0.596 Hom.: 5509

Bravo AF: 0.538

Asia WGS AF: 0.564 AC: 1963 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	5.9
DANN	Benign	0.68

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs377426; hg19: chr4-112762836;