ENST00000508313.3:n.96-16382G>A

Variant names:

• chr4-169959225-C-T
• rs10016872
• ENST00000508313.4:n.98-16382G>A

Variant summary

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

The ENST00000508313.4(LINC02275):​n.98-16382G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.501 in 152,118 control chromosomes in the GnomAD database, including 19,438 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 0.50 (19438 hom., cov: 32)
• Consequence: LINC02275 ENST00000508313.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.03
• Publications: 3 publications found

Genes affected

LINC02275 (HGNC:53191): (long intergenic non-protein coding RNA 2275)

ENSG00000251200 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.526 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000508313.4. 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
	LINC02275	NR_037878.1		n.88-16382G>A		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC02275	ENST00000508313.4	TSL:2	n.98-16382G>A		intron	N/A
	ENSG00000251200	ENST00000509956.1	TSL:2	n.250-3910C>T		intron	N/A
	LINC02275	ENST00000657085.2		n.89+16591G>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.501 AC: 76223 AN: 152000 Hom.: 19421 Cov.: 32

Gnomad AFR AF: 0.497

Gnomad AMI AF: 0.496

Gnomad AMR AF: 0.508

Gnomad ASJ AF: 0.595

Gnomad EAS AF: 0.152

Gnomad SAS AF: 0.413

Gnomad FIN AF: 0.504

Gnomad MID AF: 0.516

Gnomad NFE AF: 0.530

Gnomad OTH AF: 0.501

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

GnomAD4 genome AF: 0.501 AC: 76285 AN: 152118 Hom.: 19438 Cov.: 32 AF XY: 0.497 AC XY: 36952 AN XY: 74390

African (AFR) AF: 0.497 AC: 20621 AN: 41474

American (AMR) AF: 0.509 AC: 7785 AN: 15308

Ashkenazi Jewish (ASJ) AF: 0.595 AC: 2065 AN: 3472

East Asian (EAS) AF: 0.153 AC: 791 AN: 5172

South Asian (SAS) AF: 0.414 AC: 1997 AN: 4826

European-Finnish (FIN) AF: 0.504 AC: 5338 AN: 10584

Middle Eastern (MID) AF: 0.527 AC: 155 AN: 294

European-Non Finnish (NFE) AF: 0.530 AC: 36037 AN: 67966

Other (OTH) AF: 0.495 AC: 1046 AN: 2114

Alfa AF: 0.518 Hom.: 11196

Bravo AF: 0.498

Asia WGS AF: 0.284 AC: 988 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	1.2
DANN	Benign	0.58
PhyloP100		-1.0

Splicing

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

Other links and lift over

dbSNP: rs10016872; hg19: chr4-170880376;