rs13074058

Positions:

• chr3-185149764-C-T

Variant summary

Our verdict is Benign. Variant got -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

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

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
C3orf70	NM_001025266.3	c.196+2864G>A		intron_variant		ENST00000335012.3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
C3orf70	ENST00000335012.3	c.196+2864G>A		intron_variant		1	NM_001025266.3	P1

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

Gnomad4 AFR AF: 0.0195

Gnomad4 AMR AF: 0.0424

Gnomad4 ASJ AF: 0.0712

Gnomad4 EAS AF: 0.0127

Gnomad4 SAS AF: 0.113

Gnomad4 FIN AF: 0.0424

Gnomad4 NFE AF: 0.0904

Gnomad4 OTH AF: 0.0554

Alfa AF: 0.0832 Hom.: 272

Bravo AF: 0.0559

Asia WGS AF: 0.0650 AC: 225 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.75
CADD	Benign	6.0
DANN	Benign	0.78

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: rs13074058; hg19: chr3-184867552;