6-132955230-A-G

Variant names:

• chr6-132955230-A-G
• rs271158
• ENST00000659399.1:n.122+713A>G

Variant summary

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

The ENST00000659399.1(LINC00326):​n.122+713A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.595 in 152,028 control chromosomes in the GnomAD database, including 28,762 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 0.60 (28762 hom., cov: 32)
• Consequence: LINC00326 ENST00000659399.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0790
• Publications: 3 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=-0.75).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.826 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

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC00326	ENST00000659399.1		n.122+713A>G		intron	N/A
	LINC00326	ENST00000668229.2		n.71+713A>G		intron	N/A
	LINC00326	ENST00000669115.3		n.284+630A>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.595 AC: 90399 AN: 151910 Hom.: 28715 Cov.: 32

Gnomad AFR AF: 0.795

Gnomad AMI AF: 0.376

Gnomad AMR AF: 0.662

Gnomad ASJ AF: 0.537

Gnomad EAS AF: 0.848

Gnomad SAS AF: 0.650

Gnomad FIN AF: 0.445

Gnomad MID AF: 0.513

Gnomad NFE AF: 0.465

Gnomad OTH AF: 0.602

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

GnomAD4 genome AF: 0.595 AC: 90500 AN: 152028 Hom.: 28762 Cov.: 32 AF XY: 0.597 AC XY: 44318 AN XY: 74296

African (AFR) AF: 0.795 AC: 33003 AN: 41500

American (AMR) AF: 0.662 AC: 10102 AN: 15262

Ashkenazi Jewish (ASJ) AF: 0.537 AC: 1865 AN: 3470

East Asian (EAS) AF: 0.847 AC: 4376 AN: 5164

South Asian (SAS) AF: 0.651 AC: 3136 AN: 4820

European-Finnish (FIN) AF: 0.445 AC: 4692 AN: 10554

Middle Eastern (MID) AF: 0.514 AC: 151 AN: 294

European-Non Finnish (NFE) AF: 0.465 AC: 31564 AN: 67946

Other (OTH) AF: 0.602 AC: 1268 AN: 2106

Alfa AF: 0.541 Hom.: 12819

Bravo AF: 0.625

Asia WGS AF: 0.733 AC: 2550 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.75
CADD	Benign	6.9
DANN	Benign	0.69
PhyloP100		-0.079

Splicing

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

Other links and lift over

dbSNP: rs271158; hg19: chr6-133276369;