rs13242060

chr7-17519264-T-C

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NR_110013.1(LINC02889):n.159-35730A>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 0.101 in 152,204 control chromosomes in the GnomAD database, including 1,038 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 0.10 (1038 hom., cov: 32)
• Consequence: LINC02889 NR_110013.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.537

Genes affected

LINC02889 (HGNC:55071): (long intergenic non-protein coding RNA 2889)

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.201 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LINC02889	NR_110013.1	n.159-35730A>G		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
LINC02889	ENST00000636929.1	n.79+4833A>G		intron_variant, non_coding_transcript_variant		5

Frequencies

GnomAD3 genomes AF: 0.101 AC: 15320 AN: 152086 Hom.: 1040 Cov.: 32

Gnomad AFR AF: 0.0229

Gnomad AMI AF: 0.120

Gnomad AMR AF: 0.171

Gnomad ASJ AF: 0.130

Gnomad EAS AF: 0.119

Gnomad SAS AF: 0.212

Gnomad FIN AF: 0.141

Gnomad MID AF: 0.0823

Gnomad NFE AF: 0.115

Gnomad OTH AF: 0.108

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

GnomAD4 genome AF: 0.101 AC: 15316 AN: 152204 Hom.: 1038 Cov.: 32 AF XY: 0.106 AC XY: 7854 AN XY: 74424

Gnomad4 AFR AF: 0.0229

Gnomad4 AMR AF: 0.171

Gnomad4 ASJ AF: 0.130

Gnomad4 EAS AF: 0.119

Gnomad4 SAS AF: 0.212

Gnomad4 FIN AF: 0.141

Gnomad4 NFE AF: 0.115

Gnomad4 OTH AF: 0.108

Alfa AF: 0.112 Hom.: 219

Bravo AF: 0.0979

Asia WGS AF: 0.150 AC: 520 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
Cadd	Benign	8.2
Dann	Benign	0.57

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs13242060; hg19: chr7-17558888;