rs7623788

Variant names:

• chr3-153632327-A-G
• rs7623788
• ENST00000493214.2:n.161-27582T>C

Variant summary

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

The ENST00000493214.2(LINC02006):​n.161-27582T>C variant causes a intron 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 ENST00000493214.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.206
• Publications: 5 publications found

Genes affected

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

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000493214.2. 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
	LINC02006	NR_146713.1		n.161-27582T>C		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC02006	ENST00000493214.2	TSL:2	n.161-27582T>C		intron	N/A

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

African (AFR) AF: 0.263 AC: 10912 AN: 41470

American (AMR) AF: 0.206 AC: 3154 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.109 AC: 377 AN: 3466

East Asian (EAS) AF: 0.148 AC: 766 AN: 5166

South Asian (SAS) AF: 0.109 AC: 527 AN: 4818

European-Finnish (FIN) AF: 0.0983 AC: 1042 AN: 10596

Middle Eastern (MID) AF: 0.170 AC: 50 AN: 294

European-Non Finnish (NFE) AF: 0.138 AC: 9354 AN: 67974

Other (OTH) AF: 0.164 AC: 346 AN: 2114

Alfa AF: 0.159 Hom.: 3676

Bravo AF: 0.190

Asia WGS AF: 0.144 AC: 500 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.49
DANN	Benign	0.50
PhyloP100		-0.21

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs7623788;

hg19: chr3-153350116;