rs7737173

Variant names:

• chr5-24063344-G-A
• rs7737173
• ENST00000512559.6:n.1557+82503G>A

Variant summary

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

The ENST00000512559.6(LINC02899):​n.1557+82503G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.678 in 151,940 control chromosomes in the GnomAD database, including 35,208 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 0.68 (35208 hom., cov: 32)
• Consequence: LINC02899 ENST00000512559.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.362
• Publications: 1 publications found

Genes affected

LINC02899 (HGNC:26630): (long intergenic non-protein coding RNA 2899)

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.02).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.708 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000512559.6. 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
	LINC02899	NR_131245.1		n.1557+82503G>A		intron	N/A

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC02899	ENST00000512559.6	TSL:2	n.1557+82503G>A		intron	N/A
	LINC02899	ENST00000779573.1		n.640+85422G>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.678 AC: 102943 AN: 151822 Hom.: 35162 Cov.: 32

Gnomad AFR AF: 0.648

Gnomad AMI AF: 0.695

Gnomad AMR AF: 0.615

Gnomad ASJ AF: 0.819

Gnomad EAS AF: 0.514

Gnomad SAS AF: 0.684

Gnomad FIN AF: 0.687

Gnomad MID AF: 0.753

Gnomad NFE AF: 0.713

Gnomad OTH AF: 0.687

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

GnomAD4 genome AF: 0.678 AC: 103041 AN: 151940 Hom.: 35208 Cov.: 32 AF XY: 0.676 AC XY: 50237 AN XY: 74270

African (AFR) AF: 0.649 AC: 26870 AN: 41430

American (AMR) AF: 0.615 AC: 9397 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.819 AC: 2840 AN: 3466

East Asian (EAS) AF: 0.513 AC: 2649 AN: 5162

South Asian (SAS) AF: 0.685 AC: 3308 AN: 4828

European-Finnish (FIN) AF: 0.687 AC: 7262 AN: 10568

Middle Eastern (MID) AF: 0.772 AC: 227 AN: 294

European-Non Finnish (NFE) AF: 0.713 AC: 48396 AN: 67886

Other (OTH) AF: 0.691 AC: 1458 AN: 2110

Alfa AF: 0.688 Hom.: 4487

Bravo AF: 0.672

Asia WGS AF: 0.634 AC: 2204 AN: 3472

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.32
DANN	Benign	0.15
PhyloP100		-0.36

Splicing

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

Other links and lift over

dbSNP: rs7737173; hg19: chr5-24063453;