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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105378008	XR_001744346.1	n.1059-3528C>A		intron_variant	Intron 7 of 7

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC00326	ENST00000669115.3	n.273C>A		non_coding_transcript_exon_variant	Exon 1 of 2
LINC00326	ENST00000670829.1	n.333C>A		non_coding_transcript_exon_variant	Exon 1 of 3
LINC00326	ENST00000670892.1	n.315C>A		non_coding_transcript_exon_variant	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 v4.3

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

Other links and lift over

dbSNP: rs271156; hg19: chr6-133275728; COSMIC: COSV66717383;