rs13228338

Positions:

• chr7-17519628-G-A
• chr7-17519628-G-T

Variant summary

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

The NR_110013.1(LINC02889):​n.159-36094C>T 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 0.104 in 147,062 control chromosomes in the GnomAD database, including 1,046 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 (1046 hom., cov: 31)
• Consequence: LINC02889 NR_110013.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.280

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=-0.9).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.205 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LINC02889	NR_110013.1	n.159-36094C>T		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
LINC02889	ENST00000636929.1	n.79+4469C>T		intron_variant, non_coding_transcript_variant		5

Frequencies

GnomAD3 genomes AF: 0.104 AC: 15225 AN: 146982 Hom.: 1048 Cov.: 31

Gnomad AFR AF: 0.0237

Gnomad AMI AF: 0.126

Gnomad AMR AF: 0.180

Gnomad ASJ AF: 0.131

Gnomad EAS AF: 0.122

Gnomad SAS AF: 0.216

Gnomad FIN AF: 0.155

Gnomad MID AF: 0.0844

Gnomad NFE AF: 0.116

Gnomad OTH AF: 0.113

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

GnomAD4 genome AF: 0.104 AC: 15221 AN: 147062 Hom.: 1046 Cov.: 31 AF XY: 0.109 AC XY: 7793 AN XY: 71354

Gnomad4 AFR AF: 0.0236

Gnomad4 AMR AF: 0.180

Gnomad4 ASJ AF: 0.131

Gnomad4 EAS AF: 0.122

Gnomad4 SAS AF: 0.216

Gnomad4 FIN AF: 0.155

Gnomad4 NFE AF: 0.116

Gnomad4 OTH AF: 0.113

Alfa AF: 0.109 Hom.: 539

Bravo AF: 0.0979

Asia WGS AF: 0.150 AC: 518 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	5.9
DANN	Benign	0.47

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs13228338; hg19: chr7-17559252;