rs2994598

Positions:

• chr1-34187677-C-A

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_Moderate BA1

The ENST00000488417.2(C1orf94):​c.321-9548C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.349 in 150,798 control chromosomes in the GnomAD database, including 13,415 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 0.35 (13415 hom., cov: 28)
• Consequence: C1orf94 ENST00000488417.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 2.76

Genes affected

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

ACMG classification

Verdict is Benign. Variant got -10 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.43).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.709 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
C1orf94	NM_001134734.2	c.321-9548C>A		intron_variant		ENST00000488417.2	NP_001128206.1
C1orf94	NM_032884.5	c.-250-9548C>A		intron_variant			NP_116273.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
C1orf94	ENST00000488417.2	c.321-9548C>A		intron_variant		1	NM_001134734.2	ENSP00000435634	P1
C1orf94	ENST00000373374.7	c.-250-9548C>A		intron_variant		1		ENSP00000362472

Frequencies

GnomAD3 genomes AF: 0.349 AC: 52521 AN: 150690 Hom.: 13364 Cov.: 28

Gnomad AFR AF: 0.716

Gnomad AMI AF: 0.277

Gnomad AMR AF: 0.361

Gnomad ASJ AF: 0.142

Gnomad EAS AF: 0.230

Gnomad SAS AF: 0.265

Gnomad FIN AF: 0.228

Gnomad MID AF: 0.217

Gnomad NFE AF: 0.172

Gnomad OTH AF: 0.307

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

GnomAD4 genome AF: 0.349 AC: 52623 AN: 150798 Hom.: 13415 Cov.: 28 AF XY: 0.352 AC XY: 25857 AN XY: 73554

Gnomad4 AFR AF: 0.716

Gnomad4 AMR AF: 0.361

Gnomad4 ASJ AF: 0.142

Gnomad4 EAS AF: 0.230

Gnomad4 SAS AF: 0.265

Gnomad4 FIN AF: 0.228

Gnomad4 NFE AF: 0.172

Gnomad4 OTH AF: 0.304

Alfa AF: 0.198 Hom.: 5120

Bravo AF: 0.378

Asia WGS AF: 0.287 AC: 999 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.43
CADD	Benign	15
DANN	Benign	0.72

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: rs2994598; hg19: chr1-34653278;