rs7717572

Variant names:

• chr5-67537429-G-A
• rs7717572
• ENST00000503106.5:n.252-82362G>A

Variant summary

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

The ENST00000503106.5(LINC02997):​n.252-82362G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.123 in 104,072 control chromosomes in the GnomAD database, including 909 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 0.12 (909 hom., cov: 26)
• Consequence: LINC02997 ENST00000503106.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.526

Genes affected

LINC02997 (HGNC:56113): (long intergenic non-protein coding RNA 2997)

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.83).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.491 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC02997	ENST00000503106.5	n.252-82362G>A		intron_variant	Intron 1 of 3	4
LINC02997	ENST00000668508.1	n.123+79686G>A		intron_variant	Intron 1 of 6

Frequencies

GnomAD3 genomes AF: 0.123 AC: 12840 AN: 104034 Hom.: 908 Cov.: 26

Gnomad AFR AF: 0.147

Gnomad AMI AF: 0.120

Gnomad AMR AF: 0.143

Gnomad ASJ AF: 0.0844

Gnomad EAS AF: 0.508

Gnomad SAS AF: 0.136

Gnomad FIN AF: 0.106

Gnomad MID AF: 0.100

Gnomad NFE AF: 0.0834

Gnomad OTH AF: 0.107

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

GnomAD4 genome AF: 0.123 AC: 12851 AN: 104072 Hom.: 909 Cov.: 26 AF XY: 0.128 AC XY: 6301 AN XY: 49380

Gnomad4 AFR AF: 0.147

Gnomad4 AMR AF: 0.143

Gnomad4 ASJ AF: 0.0844

Gnomad4 EAS AF: 0.509

Gnomad4 SAS AF: 0.137

Gnomad4 FIN AF: 0.106

Gnomad4 NFE AF: 0.0834

Gnomad4 OTH AF: 0.112

Alfa AF: 0.0719 Hom.: 1109

Asia WGS AF: 0.227 AC: 787 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	1.1
DANN	Benign	0.88

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7717572; hg19: chr5-66833257;