5-67653542-C-T

Variant names:

• chr5-67653542-C-T
• rs4976108
• ENST00000503106.5:n.520+33253C>T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000514368.1(LINC02997):​n.125+33627C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.177 in 151,840 control chromosomes in the GnomAD database, including 4,260 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 0.18 (4260 hom., cov: 32)
• Consequence: LINC02997 ENST00000514368.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.00700

Genes affected

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

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.404 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC02997	ENST00000503106.5	n.520+33253C>T		intron_variant	Intron 3 of 3	4
LINC02997	ENST00000514368.1	n.125+33627C>T		intron_variant	Intron 1 of 4	3
LINC02997	ENST00000668508.1	n.248+33627C>T		intron_variant	Intron 2 of 6

Frequencies

GnomAD3 genomes AF: 0.176 AC: 26758 AN: 151720 Hom.: 4251 Cov.: 32

Gnomad AFR AF: 0.405

Gnomad AMI AF: 0.0484

Gnomad AMR AF: 0.140

Gnomad ASJ AF: 0.0651

Gnomad EAS AF: 0.419

Gnomad SAS AF: 0.107

Gnomad FIN AF: 0.0836

Gnomad MID AF: 0.0886

Gnomad NFE AF: 0.0550

Gnomad OTH AF: 0.160

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

GnomAD4 genome AF: 0.177 AC: 26801 AN: 151840 Hom.: 4260 Cov.: 32 AF XY: 0.175 AC XY: 12964 AN XY: 74200

Gnomad4 AFR AF: 0.404

Gnomad4 AMR AF: 0.140

Gnomad4 ASJ AF: 0.0651

Gnomad4 EAS AF: 0.419

Gnomad4 SAS AF: 0.108

Gnomad4 FIN AF: 0.0836

Gnomad4 NFE AF: 0.0550

Gnomad4 OTH AF: 0.163

Alfa AF: 0.0416 Hom.: 63

Bravo AF: 0.196

Asia WGS AF: 0.250 AC: 868 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	6.8
DANN	Benign	0.61

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4976108; hg19: chr5-66949370;