ENST00000659399.1:n.210+13679T>C

Variant names:

• chr6-132994665-T-C
• rs271170
• ENST00000659399.1:n.210+13679T>C

Variant summary

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

The ENST00000659399.1(LINC00326):​n.210+13679T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.745 in 152,038 control chromosomes in the GnomAD database, including 43,032 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 0.74 (43032 hom., cov: 32)
• Consequence: LINC00326 ENST00000659399.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.55
• Publications: 17 publications found

Genes affected

LINC00326 (HGNC:41926): (long intergenic non-protein coding RNA 326)

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.876 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000659399.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC00326	ENST00000659399.1		n.210+13679T>C		intron	N/A
	LINC00326	ENST00000668229.2		n.71+40148T>C		intron	N/A
	LINC00326	ENST00000669115.3		n.284+40065T>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.744 AC: 113094 AN: 151920 Hom.: 42976 Cov.: 32

Gnomad AFR AF: 0.883

Gnomad AMI AF: 0.588

Gnomad AMR AF: 0.761

Gnomad ASJ AF: 0.583

Gnomad EAS AF: 0.875

Gnomad SAS AF: 0.799

Gnomad FIN AF: 0.669

Gnomad MID AF: 0.623

Gnomad NFE AF: 0.665

Gnomad OTH AF: 0.725

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

GnomAD4 genome AF: 0.745 AC: 113207 AN: 152038 Hom.: 43032 Cov.: 32 AF XY: 0.747 AC XY: 55507 AN XY: 74312

African (AFR) AF: 0.883 AC: 36669 AN: 41506

American (AMR) AF: 0.761 AC: 11613 AN: 15258

Ashkenazi Jewish (ASJ) AF: 0.583 AC: 2024 AN: 3470

East Asian (EAS) AF: 0.876 AC: 4523 AN: 5164

South Asian (SAS) AF: 0.800 AC: 3855 AN: 4820

European-Finnish (FIN) AF: 0.669 AC: 7053 AN: 10546

Middle Eastern (MID) AF: 0.626 AC: 184 AN: 294

European-Non Finnish (NFE) AF: 0.665 AC: 45216 AN: 67954

Other (OTH) AF: 0.726 AC: 1534 AN: 2114

Alfa AF: 0.709 Hom.: 62224

Bravo AF: 0.756

Asia WGS AF: 0.831 AC: 2887 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.70
DANN	Benign	0.64
PhyloP100		-1.5

Splicing

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

Other links and lift over

dbSNP: rs271170; hg19: chr6-133315804; COSMIC: COSV71189084;