1-184471407-T-C

Variant summary

Our verdict is Benign. Variant got -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

Genes affected

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

ACMG classification

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
C1orf21	NM_030806.4	c.-124-5979T>C		intron_variant		ENST00000235307.7

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
C1orf21	ENST00000235307.7	c.-124-5979T>C		intron_variant		1	NM_030806.4	P1
C1orf21	ENST00000648109.1	c.-124-5979T>C		intron_variant, NMD_transcript_variant
C1orf21	ENST00000675061.1	c.-124-5979T>C		intron_variant, NMD_transcript_variant

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

Gnomad4 AFR AF: 0.204

Gnomad4 AMR AF: 0.0646

Gnomad4 ASJ AF: 0.0678

Gnomad4 EAS AF: 0.0145

Gnomad4 SAS AF: 0.0309

Gnomad4 FIN AF: 0.127

Gnomad4 NFE AF: 0.0829

Gnomad4 OTH AF: 0.100

Alfa AF: 0.0482 Hom.: 66

Bravo AF: 0.112

Asia WGS AF: 0.0340 AC: 119 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	2.1
Dann	Benign	0.45

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

Publications

LitVar

Other links and lift over

dbSNP: rs10489725; hg19: chr1-184440541;