rs13228338

Variant names:

• chr7-17519628-G-A
• rs13228338
• ENST00000451792.1:n.159-36094C>T

Your query was ambiguous. Multiple possible variants found:

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

Variant summary

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

The ENST00000451792.1(LINC02889):​n.159-36094C>T variant causes a intron 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 ENST00000451792.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.280
• Publications: 1 publications found

Genes affected

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

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt
LINC02889	NR_110013.1	n.159-36094C>T		intron_variant	Intron 1 of 3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC02889	ENST00000451792.1	n.159-36094C>T		intron_variant	Intron 1 of 3	3
LINC02889	ENST00000454003.2	n.52+4469C>T		intron_variant	Intron 1 of 8	3
LINC02889	ENST00000636929.1	n.79+4469C>T		intron_variant	Intron 1 of 10	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

African (AFR) AF: 0.0236 AC: 942 AN: 39894

American (AMR) AF: 0.180 AC: 2592 AN: 14368

Ashkenazi Jewish (ASJ) AF: 0.131 AC: 450 AN: 3438

East Asian (EAS) AF: 0.122 AC: 613 AN: 5036

South Asian (SAS) AF: 0.216 AC: 1009 AN: 4676

European-Finnish (FIN) AF: 0.155 AC: 1451 AN: 9360

Middle Eastern (MID) AF: 0.0739 AC: 21 AN: 284

European-Non Finnish (NFE) AF: 0.116 AC: 7806 AN: 67136

Other (OTH) AF: 0.113 AC: 226 AN: 1992

Alfa AF: 0.109 Hom.: 591

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
PhyloP100		0.28

Splicing

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

Other links and lift over

dbSNP: rs13228338; hg19: chr7-17559252;