1-172448641-A-G

Position:

• chr1-172448641-A-G

Variant summary

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

The NM_139240.4(C1orf105):​c.198+110A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.872 in 643,670 control chromosomes in the GnomAD database, including 246,059 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 0.89 (60102 hom., cov: 31)
  • Exomes 𝑓: 0.87 (185957 hom.)
• Consequence: C1orf105 NM_139240.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.07

Genes affected

C1orf105 (HGNC:29591): (chromosome 1 open reading frame 105)

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.976 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
C1orf105	NM_139240.4	c.198+110A>G		intron_variant		ENST00000367727.9	NP_640333.3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
C1orf105	ENST00000367727.9	c.198+110A>G		intron_variant		1	NM_139240.4	ENSP00000356700.4
C1orf105	ENST00000488100.6	c.111+110A>G		intron_variant		5		ENSP00000431442.1

Frequencies

GnomAD3 genomes AF: 0.886 AC: 134707 AN: 152044 Hom.: 60057 Cov.: 31

Gnomad AFR AF: 0.965

Gnomad AMI AF: 0.841

Gnomad AMR AF: 0.916

Gnomad ASJ AF: 0.939

Gnomad EAS AF: 0.999

Gnomad SAS AF: 0.945

Gnomad FIN AF: 0.766

Gnomad MID AF: 0.991

Gnomad NFE AF: 0.834

Gnomad OTH AF: 0.909

GnomAD4 exome AF: 0.867 AC: 426267 AN: 491508 Hom.: 185957 AF XY: 0.871 AC XY: 228000 AN XY: 261782

Gnomad4 AFR exome AF: 0.967

Gnomad4 AMR exome AF: 0.912

Gnomad4 ASJ exome AF: 0.936

Gnomad4 EAS exome AF: 1.00

Gnomad4 SAS exome AF: 0.936

Gnomad4 FIN exome AF: 0.778

Gnomad4 NFE exome AF: 0.839

Gnomad4 OTH exome AF: 0.879

GnomAD4 genome AF: 0.886 AC: 134811 AN: 152162 Hom.: 60102 Cov.: 31 AF XY: 0.886 AC XY: 65898 AN XY: 74402

Gnomad4 AFR AF: 0.965

Gnomad4 AMR AF: 0.915

Gnomad4 ASJ AF: 0.939

Gnomad4 EAS AF: 0.999

Gnomad4 SAS AF: 0.944

Gnomad4 FIN AF: 0.766

Gnomad4 NFE AF: 0.834

Gnomad4 OTH AF: 0.910

Alfa AF: 0.854 Hom.: 6922

Bravo AF: 0.901

Asia WGS AF: 0.968 AC: 3367 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	1.6
DANN	Benign	0.44

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: rs2157451; hg19: chr1-172417781;