chr1-34218976-T-A

Variant names:

• chr1-34218976-T-A
• rs6698707
• NM_001134734.2:c.*215T>A

Variant summary

Our verdict is Likely benign. Variant got -4 ACMG points: 0P and 4B. BP4_Strong

The NM_001134734.2(C1orf94):​c.*215T>A variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. 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: not found (cov: 0)
• Consequence: C1orf94 NM_001134734.2 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.02

Genes affected

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

ACMG classification

Verdict is Likely_benign. Variant got -4 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
C1orf94	NM_001134734.2	c.*215T>A		3_prime_UTR_variant	Exon 7 of 7	ENST00000488417.2	NP_001128206.1
C1orf94	NM_032884.5	c.*215T>A		3_prime_UTR_variant	Exon 7 of 7		NP_116273.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
C1orf94	ENST00000488417.2	c.*215T>A		3_prime_UTR_variant	Exon 7 of 7	1	NM_001134734.2	ENSP00000435634.1
C1orf94	ENST00000373374.7	c.*215T>A		3_prime_UTR_variant	Exon 7 of 7	1		ENSP00000362472.3

Frequencies

GnomAD3 genomes Cov.: 0

GnomAD4 exome Cov.: 0

GnomAD4 genome Cov.: 0

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	0.48
DANN	Benign	0.41

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: rs6698707; hg19: chr1-34684577;