rs4978890

Variant names:

• chr9-110204860-T-C
• rs4978890
• NM_001012993.3:c.193+2527A>G

Variant summary

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

The NM_001012993.3(C9orf152):​c.193+2527A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.284 in 152,048 control chromosomes in the GnomAD database, including 6,266 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 0.28 (6266 hom., cov: 32)
• Consequence: C9orf152 NM_001012993.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.22
• Publications: 7 publications found

Genes affected

C9orf152 (HGNC:31455): (chromosome 9 open reading frame 152)

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.297 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
C9orf152	NM_001012993.3	c.193+2527A>G		intron_variant	Intron 1 of 1	ENST00000400613.5	NP_001013011.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
C9orf152	ENST00000400613.5	c.193+2527A>G		intron_variant	Intron 1 of 1	1	NM_001012993.3	ENSP00000383456.4
C9orf152	ENST00000473442.1	n.94+2527A>G		intron_variant	Intron 1 of 1	3

Frequencies

GnomAD3 genomes AF: 0.285 AC: 43228 AN: 151930 Hom.: 6264 Cov.: 32

Gnomad AFR AF: 0.270

Gnomad AMI AF: 0.383

Gnomad AMR AF: 0.284

Gnomad ASJ AF: 0.215

Gnomad EAS AF: 0.198

Gnomad SAS AF: 0.249

Gnomad FIN AF: 0.321

Gnomad MID AF: 0.256

Gnomad NFE AF: 0.301

Gnomad OTH AF: 0.242

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

GnomAD4 genome AF: 0.284 AC: 43256 AN: 152048 Hom.: 6266 Cov.: 32 AF XY: 0.284 AC XY: 21082 AN XY: 74324

African (AFR) AF: 0.270 AC: 11187 AN: 41474

American (AMR) AF: 0.284 AC: 4342 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.215 AC: 748 AN: 3472

East Asian (EAS) AF: 0.197 AC: 1017 AN: 5168

South Asian (SAS) AF: 0.249 AC: 1198 AN: 4820

European-Finnish (FIN) AF: 0.321 AC: 3389 AN: 10548

Middle Eastern (MID) AF: 0.252 AC: 74 AN: 294

European-Non Finnish (NFE) AF: 0.301 AC: 20440 AN: 67968

Other (OTH) AF: 0.243 AC: 512 AN: 2110

Alfa AF: 0.291 Hom.: 12593

Bravo AF: 0.281

Asia WGS AF: 0.249 AC: 867 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.62
DANN	Benign	0.81
PhyloP100		-1.2
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs4978890; hg19: chr9-112967140;