5-67653542-C-T

Position:

• chr5-67653542-C-T

Variant summary

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

The ENST00000503106.5(LINC02997):​n.520+33253C>T variant causes a intron, non coding transcript 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 ENST00000503106.5 intron, non_coding_transcript
• 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/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
LINC02997	ENST00000503106.5	n.520+33253C>T		intron_variant, non_coding_transcript_variant		4
LINC02997	ENST00000514368.1	n.125+33627C>T		intron_variant, non_coding_transcript_variant		3
LINC02997	ENST00000668508.1	n.248+33627C>T		intron_variant, non_coding_transcript_variant

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;