rs7705123

chr5-67684048-T-C

Variant summary

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

The ENST00000503106.5(LINC02997):n.520+63759T>C 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 0.393 in 151,998 control chromosomes in the GnomAD database, including 13,455 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 0.39 (13455 hom., cov: 32)
• Consequence: LINC02997 ENST00000503106.5 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.928

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=-1.02).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.706 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
LINC02997	ENST00000503106.5	n.520+63759T>C		intron_variant, non_coding_transcript_variant		4
LINC02997	ENST00000514368.1	n.125+64133T>C		intron_variant, non_coding_transcript_variant		3
LINC02997	ENST00000668508.1	n.248+64133T>C		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.393 AC: 59642 AN: 151880 Hom.: 13424 Cov.: 32

Gnomad AFR AF: 0.573

Gnomad AMI AF: 0.198

Gnomad AMR AF: 0.430

Gnomad ASJ AF: 0.290

Gnomad EAS AF: 0.726

Gnomad SAS AF: 0.310

Gnomad FIN AF: 0.332

Gnomad MID AF: 0.304

Gnomad NFE AF: 0.273

Gnomad OTH AF: 0.393

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

GnomAD4 genome AF: 0.393 AC: 59732 AN: 151998 Hom.: 13455 Cov.: 32 AF XY: 0.395 AC XY: 29317 AN XY: 74314

Gnomad4 AFR AF: 0.574

Gnomad4 AMR AF: 0.430

Gnomad4 ASJ AF: 0.290

Gnomad4 EAS AF: 0.726

Gnomad4 SAS AF: 0.310

Gnomad4 FIN AF: 0.332

Gnomad4 NFE AF: 0.273

Gnomad4 OTH AF: 0.397

Alfa AF: 0.319 Hom.: 1105

Bravo AF: 0.414

Asia WGS AF: 0.486 AC: 1692 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	1.9
Dann	Benign	0.36

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7705123; hg19: chr5-66979876;