rs4656701

Variant names:

• chr1-169718762-G-C
• rs4656701
• ENST00000498289.5:n.851+34830G>C

Variant summary

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

The ENST00000498289.5(C1orf112):​n.851+34830G>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.309 in 151,800 control chromosomes in the GnomAD database, including 7,528 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 0.31 (7528 hom., cov: 31)
• Consequence: C1orf112 ENST00000498289.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0100

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=-0.99).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.397 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+34830G>C		intron_variant	Intron 3 of 28	2

Frequencies

GnomAD3 genomes AF: 0.309 AC: 46828 AN: 151682 Hom.: 7495 Cov.: 31

Gnomad AFR AF: 0.380

Gnomad AMI AF: 0.276

Gnomad AMR AF: 0.332

Gnomad ASJ AF: 0.342

Gnomad EAS AF: 0.331

Gnomad SAS AF: 0.411

Gnomad FIN AF: 0.269

Gnomad MID AF: 0.380

Gnomad NFE AF: 0.255

Gnomad OTH AF: 0.330

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

GnomAD4 genome AF: 0.309 AC: 46919 AN: 151800 Hom.: 7528 Cov.: 31 AF XY: 0.311 AC XY: 23086 AN XY: 74172

Gnomad4 AFR AF: 0.381

Gnomad4 AMR AF: 0.332

Gnomad4 ASJ AF: 0.342

Gnomad4 EAS AF: 0.332

Gnomad4 SAS AF: 0.412

Gnomad4 FIN AF: 0.269

Gnomad4 NFE AF: 0.255

Gnomad4 OTH AF: 0.332

Alfa AF: 0.279 Hom.: 755

Bravo AF: 0.317

Asia WGS AF: 0.381 AC: 1328 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	1.8
DANN	Benign	0.32

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4656701; hg19: chr1-169687903;