chr1-34217161-C-G

Variant names:

• chr1-34217161-C-G
• rs1564274
• NM_001134734.2:c.1722-1525C>G

Variant summary

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

The NM_001134734.2(C1orf94):​c.1722-1525C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.786 in 152,134 control chromosomes in the GnomAD database, including 47,143 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 0.79 (47143 hom., cov: 31)
• Consequence: C1orf94 NM_001134734.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.388

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=-0.93).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.848 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
C1orf94	NM_001134734.2	c.1722-1525C>G		intron_variant	Intron 6 of 6	ENST00000488417.2	NP_001128206.1
C1orf94	NM_032884.5	c.1152-1525C>G		intron_variant	Intron 6 of 6		NP_116273.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
C1orf94	ENST00000488417.2	c.1722-1525C>G		intron_variant	Intron 6 of 6	1	NM_001134734.2	ENSP00000435634.1
C1orf94	ENST00000373374.7	c.1152-1525C>G		intron_variant	Intron 6 of 6	1		ENSP00000362472.3

Frequencies

GnomAD3 genomes AF: 0.786 AC: 119465 AN: 152016 Hom.: 47105 Cov.: 31

Gnomad AFR AF: 0.839

Gnomad AMI AF: 0.733

Gnomad AMR AF: 0.804

Gnomad ASJ AF: 0.718

Gnomad EAS AF: 0.844

Gnomad SAS AF: 0.870

Gnomad FIN AF: 0.799

Gnomad MID AF: 0.810

Gnomad NFE AF: 0.741

Gnomad OTH AF: 0.777

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

GnomAD4 genome AF: 0.786 AC: 119557 AN: 152134 Hom.: 47143 Cov.: 31 AF XY: 0.792 AC XY: 58867 AN XY: 74370

Gnomad4 AFR AF: 0.840

Gnomad4 AMR AF: 0.804

Gnomad4 ASJ AF: 0.718

Gnomad4 EAS AF: 0.843

Gnomad4 SAS AF: 0.870

Gnomad4 FIN AF: 0.799

Gnomad4 NFE AF: 0.741

Gnomad4 OTH AF: 0.772

Alfa AF: 0.678 Hom.: 1941

Bravo AF: 0.787

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	0.028
DANN	Benign	0.44

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: rs1564274; hg19: chr1-34682762;