rs4363475

Variant names:

• chr1-169720233-C-T
• rs4363475
• ENST00000498289.5:n.851+36301C>T

Variant summary

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

The ENST00000498289.5(C1orf112):​n.851+36301C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0296 in 152,244 control chromosomes in the GnomAD database, including 106 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 0.030 (106 hom., cov: 32)
• Consequence: C1orf112 ENST00000498289.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -3.07

Genes affected

C1orf112 (HGNC:25565): (FIGNL1 interacting regulator of recombination and mitosis)

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.09).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.0937 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
C1orf112	ENST00000498289.5	n.851+36301C>T		intron_variant	Intron 3 of 28	2

Frequencies

GnomAD3 genomes AF: 0.0296 AC: 4496 AN: 152126 Hom.: 106 Cov.: 32

Gnomad AFR AF: 0.0529

Gnomad AMI AF: 0.0373

Gnomad AMR AF: 0.0140

Gnomad ASJ AF: 0.0107

Gnomad EAS AF: 0.0618

Gnomad SAS AF: 0.101

Gnomad FIN AF: 0.0251

Gnomad MID AF: 0.0222

Gnomad NFE AF: 0.0131

Gnomad OTH AF: 0.0239

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

GnomAD4 genome AF: 0.0296 AC: 4510 AN: 152244 Hom.: 106 Cov.: 32 AF XY: 0.0319 AC XY: 2375 AN XY: 74426

Gnomad4 AFR AF: 0.0531

Gnomad4 AMR AF: 0.0140

Gnomad4 ASJ AF: 0.0107

Gnomad4 EAS AF: 0.0616

Gnomad4 SAS AF: 0.101

Gnomad4 FIN AF: 0.0251

Gnomad4 NFE AF: 0.0131

Gnomad4 OTH AF: 0.0236

Alfa AF: 0.0185 Hom.: 8

Bravo AF: 0.0277

Asia WGS AF: 0.0790 AC: 276 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.1
CADD	Benign	0.34
DANN	Benign	0.49

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Other links and lift over

dbSNP: rs4363475; hg19: chr1-169689374;