6-133075341-A-G

Variant names:

• chr6-133075341-A-G
• rs4487594
• ENST00000664029.2:n.562-11993T>C

Variant summary

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

The ENST00000664029.2(ENSG00000286438):​n.562-11993T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.933 in 151,632 control chromosomes in the GnomAD database, including 66,189 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 0.93 (66189 hom., cov: 31)
• Consequence: ENSG00000286438 ENST00000664029.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.07
• Publications: 5 publications found

Genes affected

ENSG00000286438 (HGNC:):

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=-0.94).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.977 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000664029.2. 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
	ENSG00000286438	ENST00000664029.2		n.562-11993T>C		intron	N/A
	LINC00326	ENST00000668229.2		n.72-12439A>G		intron	N/A
	LINC00326	ENST00000669115.3		n.285-30754A>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.933 AC: 141418 AN: 151514 Hom.: 66127 Cov.: 31

Gnomad AFR AF: 0.981

Gnomad AMI AF: 0.853

Gnomad AMR AF: 0.933

Gnomad ASJ AF: 0.944

Gnomad EAS AF: 1.00

Gnomad SAS AF: 0.988

Gnomad FIN AF: 0.929

Gnomad MID AF: 0.946

Gnomad NFE AF: 0.897

Gnomad OTH AF: 0.927

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

GnomAD4 genome AF: 0.933 AC: 141539 AN: 151632 Hom.: 66189 Cov.: 31 AF XY: 0.936 AC XY: 69381 AN XY: 74110

African (AFR) AF: 0.981 AC: 40681 AN: 41452

American (AMR) AF: 0.933 AC: 14144 AN: 15164

Ashkenazi Jewish (ASJ) AF: 0.944 AC: 3263 AN: 3458

East Asian (EAS) AF: 1.00 AC: 5130 AN: 5132

South Asian (SAS) AF: 0.987 AC: 4763 AN: 4824

European-Finnish (FIN) AF: 0.929 AC: 9844 AN: 10596

Middle Eastern (MID) AF: 0.949 AC: 279 AN: 294

European-Non Finnish (NFE) AF: 0.897 AC: 60705 AN: 67698

Other (OTH) AF: 0.929 AC: 1952 AN: 2102

Alfa AF: 0.908 Hom.: 88347

Bravo AF: 0.934

Asia WGS AF: 0.994 AC: 3455 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	0.26
DANN	Benign	0.59
PhyloP100		-1.1

Splicing

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

Other links and lift over

dbSNP: rs4487594; hg19: chr6-133396480;