ENST00000443406.1:n.567-2767G>A

Variant names:

• chr7-40970951-C-T
• rs2051936
• ENST00000443406.1:n.567-2767G>A

Variant summary

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

The ENST00000443406.1(LINC01450):​n.567-2767G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.229 in 151,992 control chromosomes in the GnomAD database, including 4,961 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 0.23 (4961 hom., cov: 33)
• Consequence: LINC01450 ENST00000443406.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0230
• Publications: 1 publications found

Genes affected

LINC01450 (HGNC:50792): (long intergenic non-protein coding RNA 1450)

ENSG00000300326 (HGNC:):

SUGCT (HGNC:16001): (succinyl-CoA:glutarate-CoA transferase) This gene encodes a protein that is similar to members of the CaiB/baiF CoA-transferase protein family. Mutations in this gene are associated with glutaric aciduria type III. Alternate splicing results in multiple transcript variants. [provided by RefSeq, Jul 2010]

SUGCT Gene-Disease associations (from GenCC):

• glutaric acidemia type 3

  Inheritance: AR Classification: STRONG, MODERATE, SUPPORTIVE Submitted by: Ambry Genetics, ClinGen, Orphanet, Labcorp Genetics (formerly Invitae)

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.391 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LINC01450	NR_110831.1	n.567-2767G>A		intron_variant	Intron 1 of 2
SUGCT	XR_007060157.1	n.1344-58073C>T		intron_variant	Intron 14 of 15
SUGCT	XR_007060158.1	n.1200-58073C>T		intron_variant	Intron 13 of 14

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC01450	ENST00000443406.1	n.567-2767G>A		intron_variant	Intron 1 of 2	1
ENSG00000300326	ENST00000770933.1	n.162-795C>T		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.228 AC: 34703 AN: 151874 Hom.: 4946 Cov.: 33

Gnomad AFR AF: 0.395

Gnomad AMI AF: 0.0570

Gnomad AMR AF: 0.136

Gnomad ASJ AF: 0.188

Gnomad EAS AF: 0.250

Gnomad SAS AF: 0.283

Gnomad FIN AF: 0.213

Gnomad MID AF: 0.134

Gnomad NFE AF: 0.150

Gnomad OTH AF: 0.209

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

GnomAD4 genome AF: 0.229 AC: 34764 AN: 151992 Hom.: 4961 Cov.: 33 AF XY: 0.231 AC XY: 17141 AN XY: 74322

African (AFR) AF: 0.396 AC: 16387 AN: 41414

American (AMR) AF: 0.135 AC: 2069 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.188 AC: 652 AN: 3468

East Asian (EAS) AF: 0.251 AC: 1295 AN: 5168

South Asian (SAS) AF: 0.283 AC: 1362 AN: 4812

European-Finnish (FIN) AF: 0.213 AC: 2246 AN: 10556

Middle Eastern (MID) AF: 0.140 AC: 41 AN: 292

European-Non Finnish (NFE) AF: 0.150 AC: 10217 AN: 67984

Other (OTH) AF: 0.211 AC: 443 AN: 2104

Alfa AF: 0.181 Hom.: 595

Bravo AF: 0.228

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	2.1
DANN	Benign	0.67
PhyloP100		0.023

Splicing

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

Other links and lift over

dbSNP: rs2051936; hg19: chr7-41010550;