rs6449870

Variant names:

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

Your query was ambiguous. Multiple possible variants found:

• chr5-67503414-A-G
• chr5-67503414-A-T

Variant summary

Our verdict is Benign. Variant got -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

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=-0.91).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.818 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.252-116377A>G		intron_variant	Intron 1 of 3	4
LINC02997	ENST00000668508.1	n.123+45671A>G		intron_variant	Intron 1 of 6

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

Gnomad4 AFR AF: 0.590

Gnomad4 AMR AF: 0.529

Gnomad4 ASJ AF: 0.387

Gnomad4 EAS AF: 0.839

Gnomad4 SAS AF: 0.359

Gnomad4 FIN AF: 0.438

Gnomad4 NFE AF: 0.385

Gnomad4 OTH AF: 0.462

Alfa AF: 0.403 Hom.: 24694

Bravo AF: 0.493

Asia WGS AF: 0.581 AC: 2018 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.33
DANN	Benign	0.39

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6449870; hg19: chr5-66799242;