rs2180478

Variant names:

• chr1-230853174-G-A
• rs2180478
• NM_032800.3:c.384+2494C>T

Your query was ambiguous. Multiple possible variants found:

• chr1-230853174-G-A
• chr1-230853174-G-C
• chr1-230853174-G-T

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_032800.3(C1orf198):​c.384+2494C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.163 in 152,048 control chromosomes in the GnomAD database, including 2,427 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 0.16 (2427 hom., cov: 32)
• Consequence: C1orf198 NM_032800.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.952
• Publications: 4 publications found

Genes affected

C1orf198 (HGNC:25900): (chromosome 1 open reading frame 198) Located in cytosol. [provided by Alliance of Genome Resources, Apr 2022]

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.363 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
C1orf198	NM_032800.3	c.384+2494C>T		intron_variant	Intron 2 of 3	ENST00000366663.10	NP_116189.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
C1orf198	ENST00000366663.10	c.384+2494C>T		intron_variant	Intron 2 of 3	1	NM_032800.3	ENSP00000355623.5

Frequencies

GnomAD3 genomes AF: 0.163 AC: 24818 AN: 151930 Hom.: 2422 Cov.: 32

Gnomad AFR AF: 0.0696

Gnomad AMI AF: 0.230

Gnomad AMR AF: 0.135

Gnomad ASJ AF: 0.160

Gnomad EAS AF: 0.377

Gnomad SAS AF: 0.246

Gnomad FIN AF: 0.252

Gnomad MID AF: 0.127

Gnomad NFE AF: 0.191

Gnomad OTH AF: 0.145

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

GnomAD4 genome AF: 0.163 AC: 24827 AN: 152048 Hom.: 2427 Cov.: 32 AF XY: 0.168 AC XY: 12518 AN XY: 74296

African (AFR) AF: 0.0696 AC: 2887 AN: 41502

American (AMR) AF: 0.135 AC: 2063 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.160 AC: 555 AN: 3468

East Asian (EAS) AF: 0.377 AC: 1941 AN: 5148

South Asian (SAS) AF: 0.246 AC: 1182 AN: 4814

European-Finnish (FIN) AF: 0.252 AC: 2660 AN: 10544

Middle Eastern (MID) AF: 0.112 AC: 33 AN: 294

European-Non Finnish (NFE) AF: 0.191 AC: 12986 AN: 67990

Other (OTH) AF: 0.148 AC: 311 AN: 2104

Alfa AF: 0.174 Hom.: 4103

Bravo AF: 0.150

Asia WGS AF: 0.286 AC: 993 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	2.0
DANN	Benign	0.62
PhyloP100		-0.95
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs2180478; hg19: chr1-230988920;