NM_018325.5:c.*1469T>A

Variant names:

• chr9-27546767-A-T
• rs141012074
• NM_018325.5:c.*1469T>A

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_Strong BP6_Moderate BS2

The NM_018325.5(C9orf72):​c.*1469T>A variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00467 in 152,302 control chromosomes in the GnomAD database, including 3 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

• Frequency:
  • Genomes: 𝑓 0.0047 (3 hom., cov: 33)
  • Failed GnomAD Quality Control
• Consequence: C9orf72 NM_018325.5 3_prime_UTR
• Clinical Significance: Benign criteria provided, single submitter B:1
• Conservation: PhyloP100: 1.41

Genes affected

C9orf72 (HGNC:28337): (C9orf72-SMCR8 complex subunit) The protein encoded by this gene plays an important role in the regulation of endosomal trafficking, and has been shown to interact with Rab proteins that are involved in autophagy and endocytic transport. Expansion of a GGGGCC repeat from 2-22 copies to 700-1600 copies in the intronic sequence between alternate 5' exons in transcripts from this gene is associated with 9p-linked ALS (amyotrophic lateral sclerosis) and FTD (frontotemporal dementia) (PMID: 21944778, 21944779). Studies suggest that hexanucleotide expansions could result in the selective stabilization of repeat-containing pre-mRNA, and the accumulation of insoluble dipeptide repeat protein aggregates that could be pathogenic in FTD-ALS patients (PMID: 23393093). Alternative splicing results in multiple transcript variants encoding different isoforms. [provided by RefSeq, Jul 2016]

ACMG classification

Verdict is Benign. Variant got -10 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.8).
• BP6: Variant 9-27546767-A-T is Benign according to our data. Variant chr9-27546767-A-T is described in ClinVar as [Benign]. Clinvar id is 366484.Status of the report is criteria_provided_single_submitter, 1 stars.
• BS2: High AC in GnomAd4 at 711 AD gene.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
C9orf72	NM_018325.5	c.*1469T>A		3_prime_UTR_variant	Exon 11 of 11	ENST00000380003.8	NP_060795.1
C9orf72	NM_001256054.3	c.*1469T>A		3_prime_UTR_variant	Exon 11 of 11		NP_001242983.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
C9orf72	ENST00000380003	c.*1469T>A		3_prime_UTR_variant	Exon 11 of 11	1	NM_018325.5	ENSP00000369339.3
C9orf72	ENST00000619707	c.*1469T>A		3_prime_UTR_variant	Exon 11 of 11	1		ENSP00000482753.1
C9orf72	ENST00000488117.5	n.4596T>A		non_coding_transcript_exon_variant	Exon 10 of 10	2
C9orf72	ENST00000673600.1	n.*267+1348T>A		intron_variant	Intron 11 of 11			ENSP00000500650.1

Frequencies

GnomAD3 genomes AF: 0.00468 AC: 712 AN: 152184 Hom.: 3 Cov.: 33

Gnomad AFR AF: 0.00118

Gnomad AMI AF: 0.0164

Gnomad AMR AF: 0.00144

Gnomad ASJ AF: 0.00490

Gnomad EAS AF: 0.00115

Gnomad SAS AF: 0.00725

Gnomad FIN AF: 0.00169

Gnomad MID AF: 0.00949

Gnomad NFE AF: 0.00797

Gnomad OTH AF: 0.00239

GnomAD4 exome Data not reliable, filtered out with message: AC0 AC: 0 AN: 0 Hom.: 0 Cov.: 0 AC XY: 0 AN XY: 0

GnomAD4 genome AF: 0.00467 AC: 711 AN: 152302 Hom.: 3 Cov.: 33 AF XY: 0.00452 AC XY: 337 AN XY: 74486

Gnomad4 AFR AF: 0.00118

Gnomad4 AMR AF: 0.00144

Gnomad4 ASJ AF: 0.00490

Gnomad4 EAS AF: 0.00116

Gnomad4 SAS AF: 0.00705

Gnomad4 FIN AF: 0.00169

Gnomad4 NFE AF: 0.00797

Gnomad4 OTH AF: 0.00236

Alfa AF: 0.00283 Hom.: 0

Bravo AF: 0.00415

Asia WGS AF: 0.00260 AC: 9 AN: 3476

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

Submissions by phenotype

Frontotemporal dementia and/or amyotrophic lateral sclerosis 1 Benign:1

Jan 13, 2018

Illumina Laboratory Services, Illumina

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

This variant was observed in the ICSL laboratory as part of a predisposition screen in an ostensibly healthy population. It had not been previously curated by ICSL or reported in the Human Gene Mutation Database (HGMD: prior to June 1st, 2018), and was therefore a candidate for classification through an automated scoring system. Utilizing variant allele frequency, disease prevalence and penetrance estimates, and inheritance mode, an automated score was calculated to assess if this variant is too frequent to cause the disease. Based on the score and internal cut-off values, a variant classified as benign is not then subjected to further curation. The score for this variant resulted in a classification of benign for this disease. -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.80
CADD	Benign	3.4
DANN	Benign	0.77

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

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

Publications

LitVar

Other links and lift over

dbSNP: rs141012074; hg19: chr9-27546765;