ENST00000503106.5:n.252-82362G>A

Variant names:

• chr5-67537429-G-A
• rs7717572
• ENST00000503106.5:n.252-82362G>A

Variant summary

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

The ENST00000503106.5(LINC02997):​n.252-82362G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.123 in 104,072 control chromosomes in the GnomAD database, including 909 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 0.12 (909 hom., cov: 26)
• Consequence: LINC02997 ENST00000503106.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.526
• Publications: 10 publications found

Genes affected

LINC02997 (HGNC:56113): (long intergenic non-protein coding RNA 2997)

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.83).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.491 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000503106.5. 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
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC02997	ENST00000503106.5	TSL:4	n.252-82362G>A		intron	N/A
	LINC02997	ENST00000668508.1		n.123+79686G>A		intron	N/A
	LINC02997	ENST00000839003.1		n.108-39298G>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.123 AC: 12840 AN: 104034 Hom.: 908 Cov.: 26

Gnomad AFR AF: 0.147

Gnomad AMI AF: 0.120

Gnomad AMR AF: 0.143

Gnomad ASJ AF: 0.0844

Gnomad EAS AF: 0.508

Gnomad SAS AF: 0.136

Gnomad FIN AF: 0.106

Gnomad MID AF: 0.100

Gnomad NFE AF: 0.0834

Gnomad OTH AF: 0.107

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

GnomAD4 genome AF: 0.123 AC: 12851 AN: 104072 Hom.: 909 Cov.: 26 AF XY: 0.128 AC XY: 6301 AN XY: 49380

African (AFR) AF: 0.147 AC: 3385 AN: 23100

American (AMR) AF: 0.143 AC: 1367 AN: 9536

Ashkenazi Jewish (ASJ) AF: 0.0844 AC: 235 AN: 2784

East Asian (EAS) AF: 0.509 AC: 2096 AN: 4120

South Asian (SAS) AF: 0.137 AC: 491 AN: 3584

European-Finnish (FIN) AF: 0.106 AC: 595 AN: 5624

Middle Eastern (MID) AF: 0.107 AC: 16 AN: 150

European-Non Finnish (NFE) AF: 0.0834 AC: 4429 AN: 53110

Other (OTH) AF: 0.112 AC: 152 AN: 1356

Alfa AF: 0.0778 Hom.: 2885

Asia WGS AF: 0.227 AC: 787 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	1.1
DANN	Benign	0.88
PhyloP100		-0.53

Splicing

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

Other links and lift over

dbSNP: rs7717572; hg19: chr5-66833257;