rs2994598

Variant names:

• chr1-34187677-C-A
• rs2994598
• NM_001134734.2:c.321-9548C>A

Your query was ambiguous. Multiple possible variants found:

• chr1-34187677-C-A
• chr1-34187677-C-G
• chr1-34187677-C-T

Variant summary

Our verdict is Benign. The variant received -10 ACMG points: 0P and 10B. BP4_Moderate BA1

The NM_001134734.2(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 NM_001134734.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 2.76
• Publications: 2 publications found

Genes affected

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

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt
C1orf94	NM_001134734.2	c.321-9548C>A		intron_variant	Intron 1 of 6	ENST00000488417.2	NP_001128206.1
C1orf94	NM_032884.5	c.-250-9548C>A		intron_variant	Intron 1 of 6		NP_116273.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
C1orf94	ENST00000488417.2	c.321-9548C>A		intron_variant	Intron 1 of 6	1	NM_001134734.2	ENSP00000435634.1
C1orf94	ENST00000373374.7	c.-250-9548C>A		intron_variant	Intron 1 of 6	1		ENSP00000362472.3

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

African (AFR) AF: 0.716 AC: 29286 AN: 40890

American (AMR) AF: 0.361 AC: 5471 AN: 15152

Ashkenazi Jewish (ASJ) AF: 0.142 AC: 493 AN: 3460

East Asian (EAS) AF: 0.230 AC: 1178 AN: 5124

South Asian (SAS) AF: 0.265 AC: 1255 AN: 4744

European-Finnish (FIN) AF: 0.228 AC: 2356 AN: 10312

Middle Eastern (MID) AF: 0.212 AC: 62 AN: 292

European-Non Finnish (NFE) AF: 0.172 AC: 11638 AN: 67836

Other (OTH) AF: 0.304 AC: 634 AN: 2084

Alfa AF: 0.211 Hom.: 8045

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
PhyloP100		2.8
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: rs2994598; hg19: chr1-34653278;