rs7623788

chr3-153632327-A-G

Variant summary

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

The NR_146713.1(LINC02006):n.161-27582T>C 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 0.175 in 152,082 control chromosomes in the GnomAD database, including 2,611 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 0.18 (2611 hom., cov: 32)
• Consequence: LINC02006 NR_146713.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.206

Genes affected

LINC02006 (HGNC:52842): (long intergenic non-protein coding RNA 2006)

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.259 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LINC02006	NR_146713.1	n.161-27582T>C		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
LINC02006	ENST00000493214.2	n.161-27582T>C		intron_variant, non_coding_transcript_variant		2

Frequencies

GnomAD3 genomes AF: 0.175 AC: 26634 AN: 151964 Hom.: 2613 Cov.: 32

Gnomad AFR AF: 0.263

Gnomad AMI AF: 0.151

Gnomad AMR AF: 0.207

Gnomad ASJ AF: 0.109

Gnomad EAS AF: 0.148

Gnomad SAS AF: 0.109

Gnomad FIN AF: 0.0983

Gnomad MID AF: 0.161

Gnomad NFE AF: 0.138

Gnomad OTH AF: 0.162

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

GnomAD4 genome AF: 0.175 AC: 26665 AN: 152082 Hom.: 2611 Cov.: 32 AF XY: 0.173 AC XY: 12873 AN XY: 74362

Gnomad4 AFR AF: 0.263

Gnomad4 AMR AF: 0.206

Gnomad4 ASJ AF: 0.109

Gnomad4 EAS AF: 0.148

Gnomad4 SAS AF: 0.109

Gnomad4 FIN AF: 0.0983

Gnomad4 NFE AF: 0.138

Gnomad4 OTH AF: 0.164

Alfa AF: 0.155 Hom.: 713

Bravo AF: 0.190

Asia WGS AF: 0.144 AC: 500 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
Cadd	Benign	0.49
Dann	Benign	0.50

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7623788; hg19: chr3-153350116;