ENST00000557072.3:n.212+1317T>G

Variant names:

• chr14-98137514-T-G
• rs1461587
• ENST00000557072.3:n.212+1317T>G

Variant summary

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

The ENST00000557072.3(LINC02295):​n.212+1317T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.231 in 151,250 control chromosomes in the GnomAD database, including 4,346 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 0.23 (4346 hom., cov: 29)
• Consequence: LINC02295 ENST00000557072.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.911
• Publications: 2 publications found

Genes affected

LINC02295 (HGNC:53211): (long intergenic non-protein coding RNA 2295)

ENSG00000259097 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.298 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000557072.3. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC02295	NR_184268.1		n.211+1317T>G		intron	N/A

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC02295	ENST00000557072.3	TSL:1	n.212+1317T>G		intron	N/A
	ENSG00000259097	ENST00000555776.1	TSL:4	n.122-56989A>C		intron	N/A
	LINC02295	ENST00000684820.2		n.211+1317T>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.231 AC: 34901 AN: 151134 Hom.: 4338 Cov.: 29

Gnomad AFR AF: 0.302

Gnomad AMI AF: 0.134

Gnomad AMR AF: 0.195

Gnomad ASJ AF: 0.224

Gnomad EAS AF: 0.181

Gnomad SAS AF: 0.129

Gnomad FIN AF: 0.161

Gnomad MID AF: 0.218

Gnomad NFE AF: 0.220

Gnomad OTH AF: 0.210

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

GnomAD4 genome AF: 0.231 AC: 34959 AN: 151250 Hom.: 4346 Cov.: 29 AF XY: 0.225 AC XY: 16603 AN XY: 73862

African (AFR) AF: 0.302 AC: 12416 AN: 41096

American (AMR) AF: 0.195 AC: 2962 AN: 15212

Ashkenazi Jewish (ASJ) AF: 0.224 AC: 776 AN: 3464

East Asian (EAS) AF: 0.181 AC: 929 AN: 5130

South Asian (SAS) AF: 0.130 AC: 621 AN: 4780

European-Finnish (FIN) AF: 0.161 AC: 1692 AN: 10482

Middle Eastern (MID) AF: 0.221 AC: 64 AN: 290

European-Non Finnish (NFE) AF: 0.220 AC: 14927 AN: 67786

Other (OTH) AF: 0.214 AC: 450 AN: 2100

Alfa AF: 0.0977 Hom.: 134

Bravo AF: 0.240

Asia WGS AF: 0.189 AC: 656 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	0.068
DANN	Benign	0.26
PhyloP100		-0.91

Splicing

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

Other links and lift over

dbSNP: rs1461587; hg19: chr14-98603851;