1-184471486-C-T

Variant names:

• chr1-184471486-C-T
• rs10489726
• NM_030806.4:c.-124-5900C>T

Variant summary

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

The NM_030806.4(C1orf21):​c.-124-5900C>T 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 151,972 control chromosomes in the GnomAD database, including 1,247 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 (1247 hom., cov: 32)
• Consequence: C1orf21 NM_030806.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.10
• Publications: 4 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=-0.91).
• 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.-124-5900C>T		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.-124-5900C>T		intron	N/A	ENSP00000235307.6	Q9H246
	C1orf21	ENST00000866161.1		c.-45-5979C>T		intron	N/A	ENSP00000536220.1
	C1orf21	ENST00000866162.1		c.-45-5979C>T		intron	N/A	ENSP00000536221.1

Frequencies

GnomAD3 genomes AF: 0.113 AC: 17112 AN: 151856 Hom.: 1244 Cov.: 32

Gnomad AFR AF: 0.204

Gnomad AMI AF: 0.175

Gnomad AMR AF: 0.0644

Gnomad ASJ AF: 0.0680

Gnomad EAS AF: 0.00193

Gnomad SAS AF: 0.0308

Gnomad FIN AF: 0.127

Gnomad MID AF: 0.0443

Gnomad NFE AF: 0.0825

Gnomad OTH AF: 0.100

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

GnomAD4 genome AF: 0.113 AC: 17137 AN: 151972 Hom.: 1247 Cov.: 32 AF XY: 0.112 AC XY: 8290 AN XY: 74274

African (AFR) AF: 0.204 AC: 8421 AN: 41378

American (AMR) AF: 0.0643 AC: 982 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.0680 AC: 236 AN: 3470

East Asian (EAS) AF: 0.00194 AC: 10 AN: 5164

South Asian (SAS) AF: 0.0310 AC: 149 AN: 4804

European-Finnish (FIN) AF: 0.127 AC: 1347 AN: 10572

Middle Eastern (MID) AF: 0.0408 AC: 12 AN: 294

European-Non Finnish (NFE) AF: 0.0825 AC: 5610 AN: 67992

Other (OTH) AF: 0.0994 AC: 210 AN: 2112

Alfa AF: 0.0833 Hom.: 1939

Bravo AF: 0.111

Asia WGS AF: 0.0290 AC: 101 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.35
DANN	Benign	0.64
PhyloP100		-1.1
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: rs10489726; hg19: chr1-184440620;