1-34218976-T-C

Variant names:

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

Variant summary

Our verdict is Likely benign. The variant received -4 ACMG points: 0P and 4B. BP4_Strong

The NM_001134734.2(C1orf94):​c.*215T>C 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: 𝑓 0.000044 (0 hom., cov: 0)
  • Exomes 𝑓: 0.00057 (0 hom.)
• Consequence: C1orf94 NM_001134734.2 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.02
• Publications: 2 publications found

Genes affected

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

ACMG classification

Our verdict: Likely_benign. The variant received -4 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
C1orf94	NM_001134734.2	c.*215T>C		3_prime_UTR_variant	Exon 7 of 7	ENST00000488417.2	NP_001128206.1
C1orf94	NM_032884.5	c.*215T>C		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>C		3_prime_UTR_variant	Exon 7 of 7	1	NM_001134734.2	ENSP00000435634.1
C1orf94	ENST00000373374.7	c.*215T>C		3_prime_UTR_variant	Exon 7 of 7	1		ENSP00000362472.3

Frequencies

GnomAD3 genomes AF: 0.0000441 AC: 2 AN: 45388 Hom.: 0 Cov.: 0

Gnomad AFR AF: 0.0000465

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.00

Gnomad ASJ AF: 0.00

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.00

Gnomad FIN AF: 0.00

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.00

Gnomad OTH AF: 0.00179

GnomAD4 exome AF: 0.000569 AC: 29 AN: 50976 Hom.: 0 Cov.: 0 AF XY: 0.000505 AC XY: 13 AN XY: 25744

⚠️ The allele balance in gnomAD version 4 Exomes is significantly skewed from the expected value of 0.5.

African (AFR) AF: 0.000278 AC: 1 AN: 3602

American (AMR) AF: 0.00 AC: 0 AN: 1074

Ashkenazi Jewish (ASJ) AF: 0.000486 AC: 1 AN: 2056

East Asian (EAS) AF: 0.000805 AC: 4 AN: 4970

South Asian (SAS) AF: 0.00152 AC: 1 AN: 656

European-Finnish (FIN) AF: 0.000347 AC: 1 AN: 2878

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 270

European-Non Finnish (NFE) AF: 0.000594 AC: 19 AN: 32002

Other (OTH) AF: 0.000577 AC: 2 AN: 3468

⚠️ The allele balance in gnomAD4 Exomes is highly skewed from 0.5 (p-value = 0), which strongly suggests a high chance of mosaicism in these individuals.

GnomAD4 genome AF: 0.0000441 AC: 2 AN: 45388 Hom.: 0 Cov.: 0 AF XY: 0.00 AC XY: 0 AN XY: 21598

⚠️ The allele balance in gnomAD version 4 Genomes is significantly skewed from the expected value of 0.5.

African (AFR) AF: 0.0000465 AC: 1 AN: 21522

American (AMR) AF: 0.00 AC: 0 AN: 2690

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 912

East Asian (EAS) AF: 0.00 AC: 0 AN: 1212

South Asian (SAS) AF: 0.00 AC: 0 AN: 934

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 1704

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 88

European-Non Finnish (NFE) AF: 0.00 AC: 0 AN: 15566

Other (OTH) AF: 0.00179 AC: 1 AN: 560

⚠️ The allele balance in gnomAD version 4 Genomes is significantly skewed from the expected value of 0.5. (p-value = 0.00233887), which strongly suggests a high chance of mosaicism in these individuals.

Alfa AF: 0.474 Hom.: 27215

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	0.54
DANN	Benign	0.42
PhyloP100		-2.0
Mutation Taster		=100/0	polymorphism

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: rs6698707; hg19: chr1-34684577;