rs899379

Variant names:

• chr1-34194697-G-A
• rs899379
• NM_001134734.2:c.321-2528G>A

Your query was ambiguous. Multiple possible variants found:

• chr1-34194697-G-A
• chr1-34194697-G-C

Variant summary

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

The NM_001134734.2(C1orf94):​c.321-2528G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0658 in 151,982 control chromosomes in the GnomAD database, including 888 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 0.066 (888 hom., cov: 32)
• Consequence: C1orf94 NM_001134734.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.136
• Publications: 1 publications found

Genes affected

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

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.204 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
C1orf94	NM_001134734.2	c.321-2528G>A		intron_variant	Intron 1 of 6	ENST00000488417.2	NP_001128206.1
C1orf94	NM_032884.5	c.-250-2528G>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.321-2528G>A		intron_variant	Intron 1 of 6	1	NM_001134734.2	ENSP00000435634.1
C1orf94	ENST00000373374.7	c.-250-2528G>A		intron_variant	Intron 1 of 6	1		ENSP00000362472.3

Frequencies

GnomAD3 genomes AF: 0.0658 AC: 9993 AN: 151866 Hom.: 886 Cov.: 32

Gnomad AFR AF: 0.208

Gnomad AMI AF: 0.00548

Gnomad AMR AF: 0.0307

Gnomad ASJ AF: 0.0245

Gnomad EAS AF: 0.00270

Gnomad SAS AF: 0.0423

Gnomad FIN AF: 0.00255

Gnomad MID AF: 0.0190

Gnomad NFE AF: 0.00671

Gnomad OTH AF: 0.0631

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

GnomAD4 genome AF: 0.0658 AC: 9999 AN: 151982 Hom.: 888 Cov.: 32 AF XY: 0.0633 AC XY: 4704 AN XY: 74268

African (AFR) AF: 0.208 AC: 8608 AN: 41414

American (AMR) AF: 0.0306 AC: 467 AN: 15268

Ashkenazi Jewish (ASJ) AF: 0.0245 AC: 85 AN: 3470

East Asian (EAS) AF: 0.00271 AC: 14 AN: 5164

South Asian (SAS) AF: 0.0419 AC: 201 AN: 4796

European-Finnish (FIN) AF: 0.00255 AC: 27 AN: 10568

Middle Eastern (MID) AF: 0.0170 AC: 5 AN: 294

European-Non Finnish (NFE) AF: 0.00671 AC: 456 AN: 67998

Other (OTH) AF: 0.0624 AC: 131 AN: 2098

Alfa AF: 0.0114 Hom.: 24

Bravo AF: 0.0744

Asia WGS AF: 0.0420 AC: 146 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	4.6
DANN	Benign	0.50
PhyloP100		0.14
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: rs899379; hg19: chr1-34660298;