1-169712216-T-C

Position:

• chr1-169712216-T-C

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_Moderate BA1

The ENST00000498289.5(C1orf112):​n.851+28284T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.188 in 152,064 control chromosomes in the GnomAD database, including 2,955 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 0.19 (2955 hom., cov: 32)
• Consequence: C1orf112 ENST00000498289.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.92

Genes affected

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

ACMG classification

Verdict is Benign. Variant got -10 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.37).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.24 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
C1orf112	ENST00000498289.5	n.851+28284T>C		intron_variant		2

Frequencies

GnomAD3 genomes AF: 0.188 AC: 28544 AN: 151944 Hom.: 2946 Cov.: 32

Gnomad AFR AF: 0.243

Gnomad AMI AF: 0.141

Gnomad AMR AF: 0.246

Gnomad ASJ AF: 0.178

Gnomad EAS AF: 0.250

Gnomad SAS AF: 0.236

Gnomad FIN AF: 0.172

Gnomad MID AF: 0.247

Gnomad NFE AF: 0.136

Gnomad OTH AF: 0.210

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

GnomAD4 genome AF: 0.188 AC: 28592 AN: 152064 Hom.: 2955 Cov.: 32 AF XY: 0.190 AC XY: 14153 AN XY: 74326

Gnomad4 AFR AF: 0.243

Gnomad4 AMR AF: 0.246

Gnomad4 ASJ AF: 0.178

Gnomad4 EAS AF: 0.251

Gnomad4 SAS AF: 0.237

Gnomad4 FIN AF: 0.172

Gnomad4 NFE AF: 0.136

Gnomad4 OTH AF: 0.208

Alfa AF: 0.163 Hom.: 369

Bravo AF: 0.200

Asia WGS AF: 0.251 AC: 871 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.37
CADD	Benign	16
DANN	Benign	0.90

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2205849; hg19: chr1-169681357;