rs7717572

chr5-67537429-G-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, non coding transcript 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, non_coding_transcript
• 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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
LINC02997	ENST00000503106.5	n.252-82362G>A		intron_variant, non_coding_transcript_variant		4
LINC02997	ENST00000668508.1	n.123+79686G>A		intron_variant, non_coding_transcript_variant

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;