chr1-184471407-T-C

Variant names:

• chr1-184471407-T-C
• rs10489725
• NM_030806.4:c.-124-5979T>C

Variant summary

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

The NM_030806.4(C1orf21):​c.-124-5979T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.113 in 152,202 control chromosomes in the GnomAD database, including 1,257 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 0.11 (1257 hom., cov: 32)
• Consequence: C1orf21 NM_030806.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0930
• Publications: 3 publications found

Genes affected

C1orf21 (HGNC:15494): (chromosome 1 open reading frame 21)

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.2 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_030806.4. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	C1orf21	NM_030806.4	MANE Select	c.-124-5979T>C		intron	N/A	NP_110433.1	Q9H246

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	C1orf21	ENST00000235307.7	TSL:1 MANE Select	c.-124-5979T>C		intron	N/A	ENSP00000235307.6	Q9H246
	C1orf21	ENST00000866161.1		c.-45-6058T>C		intron	N/A	ENSP00000536220.1
	C1orf21	ENST00000866162.1		c.-45-6058T>C		intron	N/A	ENSP00000536221.1

Frequencies

GnomAD3 genomes AF: 0.113 AC: 17248 AN: 152084 Hom.: 1254 Cov.: 32

Gnomad AFR AF: 0.204

Gnomad AMI AF: 0.175

Gnomad AMR AF: 0.0647

Gnomad ASJ AF: 0.0678

Gnomad EAS AF: 0.0145

Gnomad SAS AF: 0.0306

Gnomad FIN AF: 0.127

Gnomad MID AF: 0.0475

Gnomad NFE AF: 0.0828

Gnomad OTH AF: 0.101

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

GnomAD4 genome AF: 0.113 AC: 17274 AN: 152202 Hom.: 1257 Cov.: 32 AF XY: 0.112 AC XY: 8360 AN XY: 74428

African (AFR) AF: 0.204 AC: 8460 AN: 41502

American (AMR) AF: 0.0646 AC: 988 AN: 15300

Ashkenazi Jewish (ASJ) AF: 0.0678 AC: 235 AN: 3464

East Asian (EAS) AF: 0.0145 AC: 75 AN: 5174

South Asian (SAS) AF: 0.0309 AC: 149 AN: 4826

European-Finnish (FIN) AF: 0.127 AC: 1346 AN: 10600

Middle Eastern (MID) AF: 0.0442 AC: 13 AN: 294

European-Non Finnish (NFE) AF: 0.0829 AC: 5636 AN: 68016

Other (OTH) AF: 0.100 AC: 212 AN: 2114

Alfa AF: 0.0682 Hom.: 200

Bravo AF: 0.112

Asia WGS AF: 0.0340 AC: 119 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	2.1
DANN	Benign	0.45
PhyloP100		-0.093
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: rs10489725; hg19: chr1-184440541;