chr5-67653805-G-A

Variant names:

• chr5-67653805-G-A
• rs10059317
• ENST00000503106.5:n.520+33516G>A

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000503106.5(LINC02997):​n.520+33516G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.176 in 151,984 control chromosomes in the GnomAD database, including 4,252 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 (4252 hom., cov: 32)
• Consequence: LINC02997 ENST00000503106.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.222
• Publications: 1 publications found

Genes affected

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

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.405 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000503106.5. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC02997	ENST00000503106.5	TSL:4	n.520+33516G>A		intron	N/A
	LINC02997	ENST00000514368.2	TSL:3	n.125+33890G>A		intron	N/A
	LINC02997	ENST00000668508.1		n.248+33890G>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.176 AC: 26746 AN: 151864 Hom.: 4243 Cov.: 32

Gnomad AFR AF: 0.404

Gnomad AMI AF: 0.0482

Gnomad AMR AF: 0.140

Gnomad ASJ AF: 0.0651

Gnomad EAS AF: 0.420

Gnomad SAS AF: 0.107

Gnomad FIN AF: 0.0833

Gnomad MID AF: 0.0886

Gnomad NFE AF: 0.0549

Gnomad OTH AF: 0.160

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

GnomAD4 genome AF: 0.176 AC: 26789 AN: 151984 Hom.: 4252 Cov.: 32 AF XY: 0.175 AC XY: 12974 AN XY: 74310

African (AFR) AF: 0.404 AC: 16727 AN: 41426

American (AMR) AF: 0.140 AC: 2127 AN: 15242

Ashkenazi Jewish (ASJ) AF: 0.0651 AC: 226 AN: 3470

East Asian (EAS) AF: 0.419 AC: 2165 AN: 5162

South Asian (SAS) AF: 0.107 AC: 518 AN: 4826

European-Finnish (FIN) AF: 0.0833 AC: 882 AN: 10584

Middle Eastern (MID) AF: 0.0884 AC: 26 AN: 294

European-Non Finnish (NFE) AF: 0.0549 AC: 3731 AN: 67954

Other (OTH) AF: 0.162 AC: 343 AN: 2114

Alfa AF: 0.130 Hom.: 380

Bravo AF: 0.196

Asia WGS AF: 0.250 AC: 868 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.83
DANN	Benign	0.54
PhyloP100		-0.22

Splicing

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

Other links and lift over

dbSNP: rs10059317; hg19: chr5-66949633;