4-111959258-C-T

Variant names:

• chr4-111959258-C-T
• rs2016740
• ENST00000508010.2:n.194+61156G>A

Variant summary

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

The ENST00000508010.2(LINC02945):​n.194+61156G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.371 in 152,060 control chromosomes in the GnomAD database, including 10,984 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 (10984 hom., cov: 32)
• Consequence: LINC02945 ENST00000508010.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.257
• Publications: 6 publications found

Genes affected

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=-0.81).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.496 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LINC02945	NR_186680.1	n.98+113307G>A		intron_variant	Intron 1 of 2
LINC02945	NR_186681.1	n.184+61156G>A		intron_variant	Intron 2 of 3
LINC02945	NR_186682.1	n.83-130208G>A		intron_variant	Intron 1 of 2
LINC02945	NR_186683.1	n.62+113343G>A		intron_variant	Intron 1 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC02945	ENST00000508010.2	n.194+61156G>A		intron_variant	Intron 2 of 4	5
LINC02945	ENST00000511219.1	n.134+113307G>A		intron_variant	Intron 1 of 2	3
LINC02945	ENST00000679735.2	n.187+61156G>A		intron_variant	Intron 2 of 3

Frequencies

GnomAD3 genomes AF: 0.371 AC: 56334 AN: 151942 Hom.: 10979 Cov.: 32

Gnomad AFR AF: 0.497

Gnomad AMI AF: 0.182

Gnomad AMR AF: 0.365

Gnomad ASJ AF: 0.361

Gnomad EAS AF: 0.513

Gnomad SAS AF: 0.291

Gnomad FIN AF: 0.256

Gnomad MID AF: 0.377

Gnomad NFE AF: 0.312

Gnomad OTH AF: 0.351

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

GnomAD4 genome AF: 0.371 AC: 56375 AN: 152060 Hom.: 10984 Cov.: 32 AF XY: 0.367 AC XY: 27282 AN XY: 74330

African (AFR) AF: 0.497 AC: 20586 AN: 41444

American (AMR) AF: 0.366 AC: 5589 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.361 AC: 1252 AN: 3468

East Asian (EAS) AF: 0.513 AC: 2648 AN: 5166

South Asian (SAS) AF: 0.290 AC: 1396 AN: 4820

European-Finnish (FIN) AF: 0.256 AC: 2701 AN: 10570

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

European-Non Finnish (NFE) AF: 0.312 AC: 21192 AN: 67996

Other (OTH) AF: 0.347 AC: 731 AN: 2108

Alfa AF: 0.321 Hom.: 13571

Bravo AF: 0.386

Asia WGS AF: 0.387 AC: 1345 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
CADD	Benign	6.9
DANN	Benign	0.68
PhyloP100		0.26

Splicing

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

Other links and lift over

dbSNP: rs2016740; hg19: chr4-112880414;