rs17589290

Variant names:

• chr4-112002081-C-G
• rs17589290
• ENST00000508010.2:n.194+18333G>C

Variant summary

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

The ENST00000508010.2(LINC02945):​n.194+18333G>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0289 in 152,238 control chromosomes in the GnomAD database, including 174 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 0.029 (174 hom., cov: 32)
• Consequence: LINC02945 ENST00000508010.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0480
• Publications: 12 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=-0.85).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.133 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LINC02945	NR_186680.1	n.98+70484G>C		intron_variant	Intron 1 of 2
LINC02945	NR_186681.1	n.184+18333G>C		intron_variant	Intron 2 of 3
LINC02945	NR_186682.1	n.82+110108G>C		intron_variant	Intron 1 of 2
LINC02945	NR_186683.1	n.62+70520G>C		intron_variant	Intron 1 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC02945	ENST00000508010.2	n.194+18333G>C		intron_variant	Intron 2 of 4	5
LINC02945	ENST00000511219.1	n.134+70484G>C		intron_variant	Intron 1 of 2	3
LINC02945	ENST00000679735.2	n.187+18333G>C		intron_variant	Intron 2 of 3

Frequencies

GnomAD3 genomes AF: 0.0289 AC: 4397 AN: 152120 Hom.: 175 Cov.: 32

Gnomad AFR AF: 0.0430

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0803

Gnomad ASJ AF: 0.0340

Gnomad EAS AF: 0.141

Gnomad SAS AF: 0.00642

Gnomad FIN AF: 0.0155

Gnomad MID AF: 0.0665

Gnomad NFE AF: 0.00388

Gnomad OTH AF: 0.0292

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

GnomAD4 genome AF: 0.0289 AC: 4396 AN: 152238 Hom.: 174 Cov.: 32 AF XY: 0.0306 AC XY: 2276 AN XY: 74422

African (AFR) AF: 0.0428 AC: 1778 AN: 41532

American (AMR) AF: 0.0805 AC: 1231 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.0340 AC: 118 AN: 3470

East Asian (EAS) AF: 0.141 AC: 730 AN: 5178

South Asian (SAS) AF: 0.00663 AC: 32 AN: 4824

European-Finnish (FIN) AF: 0.0155 AC: 164 AN: 10614

Middle Eastern (MID) AF: 0.0578 AC: 17 AN: 294

European-Non Finnish (NFE) AF: 0.00388 AC: 264 AN: 68018

Other (OTH) AF: 0.0294 AC: 62 AN: 2112

Alfa AF: 0.0152 Hom.: 71

Bravo AF: 0.0362

Asia WGS AF: 0.0700 AC: 243 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	4.0
DANN	Benign	0.57
PhyloP100		-0.048

Splicing

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

Other links and lift over

dbSNP: rs17589290; hg19: chr4-112923237;