rs67911569

Positions:

• chr5-67653730-G-A

Variant summary

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

The ENST00000503106.5(LINC02997):​n.520+33441G>A 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 0.0871 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 ENST00000503106.5 intron, non_coding_transcript
• 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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
LINC02997	ENST00000503106.5	n.520+33441G>A		intron_variant, non_coding_transcript_variant		4
LINC02997	ENST00000514368.1	n.125+33815G>A		intron_variant, non_coding_transcript_variant		3
LINC02997	ENST00000668508.1	n.248+33815G>A		intron_variant, non_coding_transcript_variant

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;