rs1478929

chr1-34198211-G-Achr1-34198211-G-C

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_001134734.2(C1orf94):c.1009+298G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0651 in 152,254 control chromosomes in the GnomAD database, including 873 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 0.065 (873 hom., cov: 33)
• Consequence: C1orf94 NM_001134734.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.26

Genes affected

C1orf94 (HGNC:28250): (chromosome 1 open reading frame 94)

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.201 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
C1orf94	NM_001134734.2	c.1009+298G>A		intron_variant		ENST00000488417.2
C1orf94	NM_032884.5	c.439+298G>A		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
C1orf94	ENST00000488417.2	c.1009+298G>A		intron_variant		1	NM_001134734.2	P1
C1orf94	ENST00000373374.7	c.439+298G>A		intron_variant		1

Frequencies

GnomAD3 genomes AF: 0.0651 AC: 9904 AN: 152136 Hom.: 871 Cov.: 33

Gnomad AFR AF: 0.205

Gnomad AMI AF: 0.00548

Gnomad AMR AF: 0.0306

Gnomad ASJ AF: 0.0303

Gnomad EAS AF: 0.00269

Gnomad SAS AF: 0.0420

Gnomad FIN AF: 0.00235

Gnomad MID AF: 0.0222

Gnomad NFE AF: 0.00667

Gnomad OTH AF: 0.0623

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

GnomAD4 genome AF: 0.0651 AC: 9909 AN: 152254 Hom.: 873 Cov.: 33 AF XY: 0.0627 AC XY: 4668 AN XY: 74448

Gnomad4 AFR AF: 0.205

Gnomad4 AMR AF: 0.0305

Gnomad4 ASJ AF: 0.0303

Gnomad4 EAS AF: 0.00270

Gnomad4 SAS AF: 0.0416

Gnomad4 FIN AF: 0.00235

Gnomad4 NFE AF: 0.00667

Gnomad4 OTH AF: 0.0616

Alfa AF: 0.0169 Hom.: 28

Bravo AF: 0.0736

Asia WGS AF: 0.0430 AC: 148 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
Cadd	Benign	6.0
Dann	Benign	0.52

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: rs1478929; hg19: chr1-34663812;