rs574007

Variant names:

• chr7-17464569-G-A
• rs574007
• ENST00000637807.1:c.*47-1583G>A

Variant summary

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

The ENST00000637807.1(ENSG00000283321):​c.*47-1583G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.861 in 151,918 control chromosomes in the GnomAD database, including 56,838 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 0.86 (56838 hom., cov: 30)
• Consequence: ENSG00000283321 ENST00000637807.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.78

Genes affected

ENSG00000283321 (HGNC:):

LINC02888 (HGNC:53765): (long intergenic non-protein coding RNA 2888)

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=-0.99).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.915 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LINC02889	NR_110013.1	n.344+601C>T		intron_variant	Intron 3 of 3
LINC02888	NR_110014.1	n.275-1583G>A		intron_variant	Intron 3 of 3
LINC02888	NR_110015.1	n.207-1583G>A		intron_variant	Intron 2 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000283321	ENST00000637807.1	c.*47-1583G>A		intron_variant	Intron 11 of 11	5		ENSP00000490530.1

Frequencies

GnomAD3 genomes AF: 0.861 AC: 130728 AN: 151800 Hom.: 56817 Cov.: 30

Gnomad AFR AF: 0.731

Gnomad AMI AF: 0.825

Gnomad AMR AF: 0.910

Gnomad ASJ AF: 0.882

Gnomad EAS AF: 0.849

Gnomad SAS AF: 0.795

Gnomad FIN AF: 0.942

Gnomad MID AF: 0.858

Gnomad NFE AF: 0.921

Gnomad OTH AF: 0.876

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

GnomAD4 genome AF: 0.861 AC: 130799 AN: 151918 Hom.: 56838 Cov.: 30 AF XY: 0.863 AC XY: 64056 AN XY: 74256

Gnomad4 AFR AF: 0.731

Gnomad4 AMR AF: 0.910

Gnomad4 ASJ AF: 0.882

Gnomad4 EAS AF: 0.849

Gnomad4 SAS AF: 0.794

Gnomad4 FIN AF: 0.942

Gnomad4 NFE AF: 0.921

Gnomad4 OTH AF: 0.873

Alfa AF: 0.891 Hom.: 8435

Bravo AF: 0.855

Asia WGS AF: 0.809 AC: 2799 AN: 3462

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	0.22
DANN	Benign	0.56

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs574007; hg19: chr7-17504193;