rs17044137

Variant names:

• chr4-111874141-T-A
• rs17044137
• ENST00000508010.2:n.195-45091A>T

Variant summary

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

The ENST00000508010.2(LINC02945):​n.195-45091A>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.258 in 152,010 control chromosomes in the GnomAD database, including 5,260 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 0.26 (5260 hom., cov: 31)
• Consequence: LINC02945 ENST00000508010.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.783
• Publications: 12 publications found

Genes affected

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

ENSG00000288691 (HGNC:):

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 (AFR) allele frequency at 95% confidence interval = 0.335 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LINC02945	NR_186680.1	n.99-45091A>T		intron_variant	Intron 1 of 2
LINC02945	NR_186681.1	n.185-45091A>T		intron_variant	Intron 2 of 3
LINC02945	NR_186682.1	n.83-45091A>T		intron_variant	Intron 1 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC02945	ENST00000508010.2	n.195-45091A>T		intron_variant	Intron 2 of 4	5
LINC02945	ENST00000511219.1	n.135-45091A>T		intron_variant	Intron 1 of 2	3
ENSG00000288691	ENST00000679726.1	n.170+23835T>A		intron_variant	Intron 2 of 6

Frequencies

GnomAD3 genomes AF: 0.257 AC: 39100 AN: 151892 Hom.: 5243 Cov.: 31

Gnomad AFR AF: 0.339

Gnomad AMI AF: 0.418

Gnomad AMR AF: 0.228

Gnomad ASJ AF: 0.221

Gnomad EAS AF: 0.135

Gnomad SAS AF: 0.120

Gnomad FIN AF: 0.237

Gnomad MID AF: 0.209

Gnomad NFE AF: 0.236

Gnomad OTH AF: 0.266

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

GnomAD4 genome AF: 0.258 AC: 39155 AN: 152010 Hom.: 5260 Cov.: 31 AF XY: 0.252 AC XY: 18748 AN XY: 74328

African (AFR) AF: 0.340 AC: 14071 AN: 41422

American (AMR) AF: 0.227 AC: 3474 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.221 AC: 767 AN: 3470

East Asian (EAS) AF: 0.135 AC: 697 AN: 5170

South Asian (SAS) AF: 0.120 AC: 580 AN: 4822

European-Finnish (FIN) AF: 0.237 AC: 2502 AN: 10574

Middle Eastern (MID) AF: 0.190 AC: 56 AN: 294

European-Non Finnish (NFE) AF: 0.236 AC: 16066 AN: 67966

Other (OTH) AF: 0.266 AC: 561 AN: 2108

Alfa AF: 0.242 Hom.: 550

Bravo AF: 0.262

Asia WGS AF: 0.149 AC: 525 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	9.2
DANN	Benign	0.55
PhyloP100		0.78

Splicing

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

Other links and lift over

dbSNP: rs17044137; hg19: chr4-112795297;