rs67911569

Variant names:

• chr5-67653730-G-A
• rs67911569
• ENST00000503106.5:n.520+33441G>A

Variant summary

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

The ENST00000514368.1(LINC02997):​n.125+33815G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0871 in 152,130 control chromosomes in the GnomAD database, including 898 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 0.087 (898 hom., cov: 32)
• Consequence: LINC02997 ENST00000514368.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.48

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=-0.98).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.294 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+33441G>A		intron_variant	Intron 3 of 3	4
LINC02997	ENST00000514368.1	n.125+33815G>A		intron_variant	Intron 1 of 4	3
LINC02997	ENST00000668508.1	n.248+33815G>A		intron_variant	Intron 2 of 6

Frequencies

GnomAD3 genomes AF: 0.0869 AC: 13217 AN: 152012 Hom.: 892 Cov.: 32

Gnomad AFR AF: 0.0290

Gnomad AMI AF: 0.0197

Gnomad AMR AF: 0.169

Gnomad ASJ AF: 0.0557

Gnomad EAS AF: 0.307

Gnomad SAS AF: 0.0818

Gnomad FIN AF: 0.0956

Gnomad MID AF: 0.0253

Gnomad NFE AF: 0.0889

Gnomad OTH AF: 0.0916

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

GnomAD4 genome AF: 0.0871 AC: 13244 AN: 152130 Hom.: 898 Cov.: 32 AF XY: 0.0895 AC XY: 6660 AN XY: 74396

Gnomad4 AFR AF: 0.0293

Gnomad4 AMR AF: 0.169

Gnomad4 ASJ AF: 0.0557

Gnomad4 EAS AF: 0.306

Gnomad4 SAS AF: 0.0814

Gnomad4 FIN AF: 0.0956

Gnomad4 NFE AF: 0.0889

Gnomad4 OTH AF: 0.0949

Alfa AF: 0.0788 Hom.: 154

Bravo AF: 0.0914

Asia WGS AF: 0.175 AC: 608 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	0.12
DANN	Benign	0.57

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs67911569; hg19: chr5-66949558;