rs6449870

Positions:

• 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, non coding transcript 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, non_coding_transcript
• 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/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
LINC02997	ENST00000503106.5	n.252-116377A>G		intron_variant, non_coding_transcript_variant		4
LINC02997	ENST00000668508.1	n.123+45671A>G		intron_variant, non_coding_transcript_variant

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;