rs271156

Variant names:

• chr6-132954589-C-A
• rs271156
• ENST00000669115.3:n.273C>A

Variant summary

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

The ENST00000669115.3(LINC00326):​n.273C>A variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.466 in 152,146 control chromosomes in the GnomAD database, including 16,720 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 0.47 (16720 hom., cov: 33)
• Consequence: LINC00326 ENST00000669115.3 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.378
• Publications: 8 publications found

Genes affected

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

LOC105378008 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.82).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.701 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000669115.3. 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
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC00326	ENST00000669115.3		n.273C>A		non_coding_transcript_exon	Exon 1 of 2
	LINC00326	ENST00000670829.1		n.333C>A		non_coding_transcript_exon	Exon 1 of 3
	LINC00326	ENST00000670892.1		n.315C>A		non_coding_transcript_exon	Exon 1 of 4

Frequencies

GnomAD3 genomes AF: 0.466 AC: 70798 AN: 152028 Hom.: 16702 Cov.: 33

Gnomad AFR AF: 0.456

Gnomad AMI AF: 0.375

Gnomad AMR AF: 0.547

Gnomad ASJ AF: 0.490

Gnomad EAS AF: 0.721

Gnomad SAS AF: 0.521

Gnomad FIN AF: 0.440

Gnomad MID AF: 0.437

Gnomad NFE AF: 0.433

Gnomad OTH AF: 0.482

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

GnomAD4 genome AF: 0.466 AC: 70850 AN: 152146 Hom.: 16720 Cov.: 33 AF XY: 0.471 AC XY: 35030 AN XY: 74362

African (AFR) AF: 0.456 AC: 18935 AN: 41530

American (AMR) AF: 0.548 AC: 8375 AN: 15296

Ashkenazi Jewish (ASJ) AF: 0.490 AC: 1702 AN: 3470

East Asian (EAS) AF: 0.720 AC: 3728 AN: 5178

South Asian (SAS) AF: 0.521 AC: 2513 AN: 4822

European-Finnish (FIN) AF: 0.440 AC: 4649 AN: 10558

Middle Eastern (MID) AF: 0.435 AC: 128 AN: 294

European-Non Finnish (NFE) AF: 0.433 AC: 29457 AN: 67972

Other (OTH) AF: 0.483 AC: 1021 AN: 2114

Alfa AF: 0.452 Hom.: 50662

Bravo AF: 0.481

Asia WGS AF: 0.582 AC: 2024 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	7.6
DANN	Benign	0.37
PhyloP100		0.38

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: rs271156;

hg19: chr6-133275728;

COSMIC: COSV66717383;