chr4-111959712-C-G

Variant names:

• chr4-111959712-C-G
• rs877936
• ENST00000681662.1:n.129C>G

Variant summary

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

The ENST00000681662.1(ENSG00000288685):​n.129C>G 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 0.372 in 152,006 control chromosomes in the GnomAD database, including 11,025 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 0.37 (11025 hom., cov: 32)
• Consequence: ENSG00000288685 ENST00000681662.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.317

Genes affected

ENSG00000288685 (HGNC:):

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=-0.9).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.495 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LINC02945	NR_186680.1	n.98+112853G>C		intron_variant	Intron 1 of 2
LINC02945	NR_186681.1	n.184+60702G>C		intron_variant	Intron 2 of 3
LINC02945	NR_186682.1	n.83-130662G>C		intron_variant	Intron 1 of 2
LINC02945	NR_186683.1	n.62+112889G>C		intron_variant	Intron 1 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000288685	ENST00000681662.1	n.129C>G		non_coding_transcript_exon_variant	Exon 1 of 3
LINC02945	ENST00000511219.1	n.134+112853G>C		intron_variant	Intron 1 of 2	3
LINC02945	ENST00000679735.1	n.187+60702G>C		intron_variant	Intron 2 of 3

Frequencies

GnomAD3 genomes AF: 0.372 AC: 56469 AN: 151886 Hom.: 11023 Cov.: 32

Gnomad AFR AF: 0.494

Gnomad AMI AF: 0.182

Gnomad AMR AF: 0.371

Gnomad ASJ AF: 0.371

Gnomad EAS AF: 0.512

Gnomad SAS AF: 0.291

Gnomad FIN AF: 0.256

Gnomad MID AF: 0.377

Gnomad NFE AF: 0.313

Gnomad OTH AF: 0.356

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

GnomAD4 genome AF: 0.372 AC: 56496 AN: 152006 Hom.: 11025 Cov.: 32 AF XY: 0.368 AC XY: 27324 AN XY: 74302

Gnomad4 AFR AF: 0.494

Gnomad4 AMR AF: 0.371

Gnomad4 ASJ AF: 0.371

Gnomad4 EAS AF: 0.512

Gnomad4 SAS AF: 0.290

Gnomad4 FIN AF: 0.256

Gnomad4 NFE AF: 0.313

Gnomad4 OTH AF: 0.352

Alfa AF: 0.207 Hom.: 423

Bravo AF: 0.387

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	1.1
DANN	Benign	0.63

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs877936; hg19: chr4-112880868;