chr1-230867468-A-C

Position:

• chr1-230867468-A-C

Variant summary

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

The NM_032800.3(C1orf198):​c.333+712T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.255 in 152,064 control chromosomes in the GnomAD database, including 5,541 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 0.25 (5541 hom., cov: 32)
• Consequence: C1orf198 NM_032800.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.629

Genes affected

C1orf198 (HGNC:25900): (chromosome 1 open reading frame 198) Located in cytosol. [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=-0.82).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.312 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
C1orf198	NM_032800.3	c.333+712T>G		intron_variant		ENST00000366663.10

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
C1orf198	ENST00000366663.10	c.333+712T>G		intron_variant		1	NM_032800.3	P1
C1orf198	ENST00000427697.2	c.-229+1344T>G		intron_variant		2
C1orf198	ENST00000470540.5	c.219+712T>G		intron_variant		2
C1orf198	ENST00000522201.1	c.204+712T>G		intron_variant		3

Frequencies

GnomAD3 genomes AF: 0.255 AC: 38691 AN: 151946 Hom.: 5541 Cov.: 32

Gnomad AFR AF: 0.161

Gnomad AMI AF: 0.338

Gnomad AMR AF: 0.290

Gnomad ASJ AF: 0.358

Gnomad EAS AF: 0.0282

Gnomad SAS AF: 0.273

Gnomad FIN AF: 0.224

Gnomad MID AF: 0.415

Gnomad NFE AF: 0.316

Gnomad OTH AF: 0.302

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

GnomAD4 genome AF: 0.255 AC: 38701 AN: 152064 Hom.: 5541 Cov.: 32 AF XY: 0.250 AC XY: 18587 AN XY: 74324

Gnomad4 AFR AF: 0.161

Gnomad4 AMR AF: 0.290

Gnomad4 ASJ AF: 0.358

Gnomad4 EAS AF: 0.0280

Gnomad4 SAS AF: 0.273

Gnomad4 FIN AF: 0.224

Gnomad4 NFE AF: 0.316

Gnomad4 OTH AF: 0.301

Alfa AF: 0.283 Hom.: 3159

Bravo AF: 0.253

Asia WGS AF: 0.178 AC: 617 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	6.4
DANN	Benign	0.59

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: rs1202585; hg19: chr1-231003214;