chr1-184471486-C-T

Position:

• chr1-184471486-C-T

Variant summary

Our verdict is Benign. Variant got -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

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=-0.91).
• 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	Protein	UniProt
C1orf21	NM_030806.4	c.-124-5900C>T		intron_variant		ENST00000235307.7	NP_110433.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
C1orf21	ENST00000235307.7	c.-124-5900C>T		intron_variant		1	NM_030806.4	ENSP00000235307.6
C1orf21	ENST00000648109.1	n.-124-5900C>T		intron_variant				ENSP00000498051.1
C1orf21	ENST00000675061.1	n.-124-5900C>T		intron_variant				ENSP00000501948.1

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

Gnomad4 AFR AF: 0.204

Gnomad4 AMR AF: 0.0643

Gnomad4 ASJ AF: 0.0680

Gnomad4 EAS AF: 0.00194

Gnomad4 SAS AF: 0.0310

Gnomad4 FIN AF: 0.127

Gnomad4 NFE AF: 0.0825

Gnomad4 OTH AF: 0.0994

Alfa AF: 0.0744 Hom.: 932

Bravo AF: 0.111

Asia WGS AF: 0.0290 AC: 101 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	0.35
DANN	Benign	0.64

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: rs10489726; hg19: chr1-184440620;