NM_030806.4:c.-124-44012A>G

Variant names:

• chr1-184433374-A-G
• rs16823149
• NM_030806.4:c.-124-44012A>G

Variant summary

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

The NM_030806.4(C1orf21):​c.-124-44012A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.153 in 152,200 control chromosomes in the GnomAD database, including 1,845 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 0.15 (1845 hom., cov: 32)
• Consequence: C1orf21 NM_030806.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.242
• Publications: 2 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 = 0.171 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
C1orf21	NM_030806.4	c.-124-44012A>G		intron_variant	Intron 1 of 5	ENST00000235307.7	NP_110433.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
C1orf21	ENST00000235307.7	c.-124-44012A>G		intron_variant	Intron 1 of 5	1	NM_030806.4	ENSP00000235307.6
C1orf21	ENST00000648109.1	n.-124-44012A>G		intron_variant	Intron 1 of 6			ENSP00000498051.1
C1orf21	ENST00000675061.1	n.-124-44012A>G		intron_variant	Intron 1 of 5			ENSP00000501948.1

Frequencies

GnomAD3 genomes AF: 0.153 AC: 23214 AN: 152082 Hom.: 1843 Cov.: 32

Gnomad AFR AF: 0.175

Gnomad AMI AF: 0.224

Gnomad AMR AF: 0.150

Gnomad ASJ AF: 0.160

Gnomad EAS AF: 0.153

Gnomad SAS AF: 0.114

Gnomad FIN AF: 0.140

Gnomad MID AF: 0.158

Gnomad NFE AF: 0.143

Gnomad OTH AF: 0.163

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

GnomAD4 genome AF: 0.153 AC: 23240 AN: 152200 Hom.: 1845 Cov.: 32 AF XY: 0.151 AC XY: 11245 AN XY: 74432

African (AFR) AF: 0.175 AC: 7250 AN: 41528

American (AMR) AF: 0.151 AC: 2299 AN: 15264

Ashkenazi Jewish (ASJ) AF: 0.160 AC: 554 AN: 3470

East Asian (EAS) AF: 0.153 AC: 795 AN: 5186

South Asian (SAS) AF: 0.114 AC: 550 AN: 4822

European-Finnish (FIN) AF: 0.140 AC: 1490 AN: 10610

Middle Eastern (MID) AF: 0.153 AC: 45 AN: 294

European-Non Finnish (NFE) AF: 0.143 AC: 9710 AN: 68002

Other (OTH) AF: 0.162 AC: 343 AN: 2114

Alfa AF: 0.107 Hom.: 218

Bravo AF: 0.153

Asia WGS AF: 0.135 AC: 471 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	2.4
DANN	Benign	0.45
PhyloP100		0.24
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: rs16823149; hg19: chr1-184402508;