rs13074058

Variant names:

• chr3-185149764-C-T
• rs13074058
• NM_001025266.3:c.196+2864G>A

Variant summary

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

The NM_001025266.3(C3orf70):​c.196+2864G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0598 in 152,290 control chromosomes in the GnomAD database, including 384 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 0.060 (384 hom., cov: 32)
• Consequence: C3orf70 NM_001025266.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.257
• Publications: 5 publications found

Genes affected

C3orf70 (HGNC:33731): (chromosome 3 open reading frame 70) Predicted to be involved in circadian behavior and nervous system development. [provided by Alliance of Genome Resources, Apr 2022]

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.75).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.105 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001025266.3. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	C3orf70	NM_001025266.3	MANE Select	c.196+2864G>A		intron	N/A	NP_001020437.1	A6NLC5

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	C3orf70	ENST00000335012.3	TSL:1 MANE Select	c.196+2864G>A		intron	N/A	ENSP00000334974.2	A6NLC5

Frequencies

GnomAD3 genomes AF: 0.0599 AC: 9109 AN: 152172 Hom.: 386 Cov.: 32

Gnomad AFR AF: 0.0195

Gnomad AMI AF: 0.0615

Gnomad AMR AF: 0.0424

Gnomad ASJ AF: 0.0712

Gnomad EAS AF: 0.0129

Gnomad SAS AF: 0.114

Gnomad FIN AF: 0.0424

Gnomad MID AF: 0.0633

Gnomad NFE AF: 0.0904

Gnomad OTH AF: 0.0560

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

GnomAD4 genome AF: 0.0598 AC: 9107 AN: 152290 Hom.: 384 Cov.: 32 AF XY: 0.0584 AC XY: 4349 AN XY: 74470

African (AFR) AF: 0.0195 AC: 812 AN: 41576

American (AMR) AF: 0.0424 AC: 648 AN: 15296

Ashkenazi Jewish (ASJ) AF: 0.0712 AC: 247 AN: 3470

East Asian (EAS) AF: 0.0127 AC: 66 AN: 5182

South Asian (SAS) AF: 0.113 AC: 544 AN: 4824

European-Finnish (FIN) AF: 0.0424 AC: 450 AN: 10610

Middle Eastern (MID) AF: 0.0680 AC: 20 AN: 294

European-Non Finnish (NFE) AF: 0.0904 AC: 6147 AN: 68016

Other (OTH) AF: 0.0554 AC: 117 AN: 2112

Alfa AF: 0.0832 Hom.: 299

Bravo AF: 0.0559

Asia WGS AF: 0.0650 AC: 225 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.75
CADD	Benign	6.0
DANN	Benign	0.78
PhyloP100		0.26
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: rs13074058; hg19: chr3-184867552;