7-17526629-T-C

Variant names:

• chr7-17526629-T-C
• rs1375237
• ENST00000451792.1:n.158+32123A>G

Variant summary

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

The ENST00000451792.1(LINC02889):​n.158+32123A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.606 in 151,822 control chromosomes in the GnomAD database, including 28,035 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 0.61 (28035 hom., cov: 31)
• Consequence: LINC02889 ENST00000451792.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.611
• Publications: 2 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=-0.85).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.628 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000451792.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC02889	NR_110013.1		n.158+32123A>G		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC02889	ENST00000451792.1	TSL:3	n.158+32123A>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.606 AC: 91875 AN: 151704 Hom.: 28016 Cov.: 31

Gnomad AFR AF: 0.619

Gnomad AMI AF: 0.622

Gnomad AMR AF: 0.638

Gnomad ASJ AF: 0.611

Gnomad EAS AF: 0.632

Gnomad SAS AF: 0.552

Gnomad FIN AF: 0.606

Gnomad MID AF: 0.703

Gnomad NFE AF: 0.590

Gnomad OTH AF: 0.618

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

GnomAD4 genome AF: 0.606 AC: 91945 AN: 151822 Hom.: 28035 Cov.: 31 AF XY: 0.604 AC XY: 44855 AN XY: 74216

African (AFR) AF: 0.619 AC: 25603 AN: 41366

American (AMR) AF: 0.638 AC: 9732 AN: 15244

Ashkenazi Jewish (ASJ) AF: 0.611 AC: 2119 AN: 3470

East Asian (EAS) AF: 0.632 AC: 3263 AN: 5162

South Asian (SAS) AF: 0.552 AC: 2656 AN: 4810

European-Finnish (FIN) AF: 0.606 AC: 6400 AN: 10554

Middle Eastern (MID) AF: 0.711 AC: 209 AN: 294

European-Non Finnish (NFE) AF: 0.590 AC: 40103 AN: 67918

Other (OTH) AF: 0.618 AC: 1299 AN: 2102

Alfa AF: 0.582 Hom.: 3304

Bravo AF: 0.613

Asia WGS AF: 0.614 AC: 2135 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	4.9
DANN	Benign	0.55
PhyloP100		0.61

Splicing

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

Other links and lift over

dbSNP: rs1375237; hg19: chr7-17566253;