4-111959712-C-G

Variant names:

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

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 1 publications found

Genes affected

ENSG00000288685 (HGNC:):

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

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000681662.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC02945	NR_186680.1		n.98+112853G>C		intron	N/A
	LINC02945	NR_186681.1		n.184+60702G>C		intron	N/A
	LINC02945	NR_186682.1		n.83-130662G>C		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000288685	ENST00000681662.1		n.129C>G		non_coding_transcript_exon	Exon 1 of 3
	LINC02945	ENST00000508010.2	TSL:5	n.194+60702G>C		intron	N/A
	LINC02945	ENST00000511219.1	TSL:3	n.134+112853G>C		intron	N/A

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

African (AFR) AF: 0.494 AC: 20478 AN: 41454

American (AMR) AF: 0.371 AC: 5671 AN: 15268

Ashkenazi Jewish (ASJ) AF: 0.371 AC: 1287 AN: 3470

East Asian (EAS) AF: 0.512 AC: 2641 AN: 5162

South Asian (SAS) AF: 0.290 AC: 1392 AN: 4808

European-Finnish (FIN) AF: 0.256 AC: 2703 AN: 10558

Middle Eastern (MID) AF: 0.388 AC: 114 AN: 294

European-Non Finnish (NFE) AF: 0.313 AC: 21302 AN: 67970

Other (OTH) AF: 0.352 AC: 742 AN: 2110

Alfa AF: 0.207 Hom.: 423

Bravo AF: 0.387

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	1.1
DANN	Benign	0.63
PhyloP100		-0.32

Splicing

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

Other links and lift over

dbSNP: rs877936; hg19: chr4-112880868;