rs10489728

Variant names:

• chr1-184515576-A-C
• rs10489728
• NM_030806.4:c.189+7894A>C

Your query was ambiguous. Multiple possible variants found:

• chr1-184515576-A-C
• chr1-184515576-A-G

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BS1 BS2

The NM_030806.4(C1orf21):​c.189+7894A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0173 in 152,312 control chromosomes in the GnomAD database, including 36 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 0.017 (36 hom., cov: 33)
• Consequence: C1orf21 NM_030806.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.452
• Publications: 0 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).
• BS1: Variant frequency is greater than expected in population afr. GnomAd4 allele frequency = 0.0173 (2638/152312) while in subpopulation AFR AF = 0.0345 (1436/41574). AF 95% confidence interval is 0.0331. There are 36 homozygotes in GnomAd4. There are 1226 alleles in the male GnomAd4 subpopulation. Median coverage is 33. This position passed quality control check.
• BS2: High Homozygotes in GnomAd4 at 36 gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
C1orf21	NM_030806.4	c.189+7894A>C		intron_variant	Intron 3 of 5	ENST00000235307.7	NP_110433.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
C1orf21	ENST00000235307.7	c.189+7894A>C		intron_variant	Intron 3 of 5	1	NM_030806.4	ENSP00000235307.6

Frequencies

GnomAD3 genomes AF: 0.0173 AC: 2635 AN: 152194 Hom.: 36 Cov.: 33

Gnomad AFR AF: 0.0346

Gnomad AMI AF: 0.00219

Gnomad AMR AF: 0.0109

Gnomad ASJ AF: 0.00634

Gnomad EAS AF: 0.0133

Gnomad SAS AF: 0.0153

Gnomad FIN AF: 0.00104

Gnomad MID AF: 0.0222

Gnomad NFE AF: 0.0119

Gnomad OTH AF: 0.0187

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

GnomAD4 genome AF: 0.0173 AC: 2638 AN: 152312 Hom.: 36 Cov.: 33 AF XY: 0.0165 AC XY: 1226 AN XY: 74486

African (AFR) AF: 0.0345 AC: 1436 AN: 41574

American (AMR) AF: 0.0109 AC: 166 AN: 15296

Ashkenazi Jewish (ASJ) AF: 0.00634 AC: 22 AN: 3468

East Asian (EAS) AF: 0.0133 AC: 69 AN: 5182

South Asian (SAS) AF: 0.0153 AC: 74 AN: 4822

European-Finnish (FIN) AF: 0.00104 AC: 11 AN: 10624

Middle Eastern (MID) AF: 0.0238 AC: 7 AN: 294

European-Non Finnish (NFE) AF: 0.0119 AC: 812 AN: 68028

Other (OTH) AF: 0.0185 AC: 39 AN: 2112

Alfa AF: 0.00512 Hom.: 2

Bravo AF: 0.0194

Asia WGS AF: 0.0120 AC: 43 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	7.3
DANN	Benign	0.48
PhyloP100		0.45
Mutation Taster		=100/0	polymorphism

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.010		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: rs10489728; hg19: chr1-184484710;