5-67503414-A-G

Variant names:

• chr5-67503414-A-G
• rs6449870
• ENST00000503106.5:n.252-116377A>G

Variant summary

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

The ENST00000503106.5(LINC02997):​n.252-116377A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.475 in 152,050 control chromosomes in the GnomAD database, including 18,216 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 0.47 (18216 hom., cov: 32)
• Consequence: LINC02997 ENST00000503106.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.34
• Publications: 3 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 = 0.818 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.252-116377A>G		intron	N/A
	LINC02997	ENST00000668508.1		n.123+45671A>G		intron	N/A
	LINC02997	ENST00000839003.1		n.107+12106A>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.474 AC: 72077 AN: 151932 Hom.: 18170 Cov.: 32

Gnomad AFR AF: 0.589

Gnomad AMI AF: 0.400

Gnomad AMR AF: 0.529

Gnomad ASJ AF: 0.387

Gnomad EAS AF: 0.839

Gnomad SAS AF: 0.359

Gnomad FIN AF: 0.438

Gnomad MID AF: 0.322

Gnomad NFE AF: 0.385

Gnomad OTH AF: 0.459

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

GnomAD4 genome AF: 0.475 AC: 72184 AN: 152050 Hom.: 18216 Cov.: 32 AF XY: 0.477 AC XY: 35421 AN XY: 74310

African (AFR) AF: 0.590 AC: 24439 AN: 41448

American (AMR) AF: 0.529 AC: 8077 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.387 AC: 1342 AN: 3466

East Asian (EAS) AF: 0.839 AC: 4344 AN: 5176

South Asian (SAS) AF: 0.359 AC: 1734 AN: 4824

European-Finnish (FIN) AF: 0.438 AC: 4629 AN: 10574

Middle Eastern (MID) AF: 0.332 AC: 97 AN: 292

European-Non Finnish (NFE) AF: 0.385 AC: 26183 AN: 67974

Other (OTH) AF: 0.462 AC: 975 AN: 2112

Alfa AF: 0.416 Hom.: 56847

Bravo AF: 0.493

Asia WGS AF: 0.581 AC: 2018 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	0.33
DANN	Benign	0.39
PhyloP100		-1.3

Splicing

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

Other links and lift over

dbSNP: rs6449870; hg19: chr5-66799242;