rs271156

Positions:

• chr6-132954589-C-A

Variant summary

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

The ENST00000670892.1(LINC00326):​n.315C>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 ENST00000670892.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.378

Genes affected

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

LOC105378008 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	UniProt
LOC105378008	XR_001744346.1	n.1059-3528C>A		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
LINC00326	ENST00000670892.1	n.315C>A		non_coding_transcript_exon_variant	1/4

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

Gnomad4 AFR AF: 0.456

Gnomad4 AMR AF: 0.548

Gnomad4 ASJ AF: 0.490

Gnomad4 EAS AF: 0.720

Gnomad4 SAS AF: 0.521

Gnomad4 FIN AF: 0.440

Gnomad4 NFE AF: 0.433

Gnomad4 OTH AF: 0.483

Alfa AF: 0.448 Hom.: 31637

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

Splicing

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

Publications

LitVar

Other links and lift over

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