rs1535133

Variant names:

• chr1-184468300-C-A
• rs1535133
• NM_030806.4:c.-124-9086C>A

Variant summary

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

The NM_030806.4(C1orf21):​c.-124-9086C>A 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 151,974 control chromosomes in the GnomAD database, including 1,238 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 (1238 hom., cov: 32)
• Consequence: C1orf21 NM_030806.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.462
• Publications: 1 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=-0.9).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.198 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
C1orf21	NM_030806.4	c.-124-9086C>A		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.-124-9086C>A		intron_variant	Intron 1 of 5	1	NM_030806.4	ENSP00000235307.6
C1orf21	ENST00000648109.1	n.-124-9086C>A		intron_variant	Intron 1 of 6			ENSP00000498051.1
C1orf21	ENST00000675061.1	n.-124-9086C>A		intron_variant	Intron 1 of 5			ENSP00000501948.1

Frequencies

GnomAD3 genomes AF: 0.113 AC: 17135 AN: 151856 Hom.: 1235 Cov.: 32

Gnomad AFR AF: 0.202

Gnomad AMI AF: 0.174

Gnomad AMR AF: 0.0642

Gnomad ASJ AF: 0.0675

Gnomad EAS AF: 0.0145

Gnomad SAS AF: 0.0313

Gnomad FIN AF: 0.127

Gnomad MID AF: 0.0475

Gnomad NFE AF: 0.0830

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: 17161 AN: 151974 Hom.: 1238 Cov.: 32 AF XY: 0.112 AC XY: 8324 AN XY: 74274

African (AFR) AF: 0.202 AC: 8357 AN: 41430

American (AMR) AF: 0.0641 AC: 979 AN: 15264

Ashkenazi Jewish (ASJ) AF: 0.0675 AC: 234 AN: 3468

East Asian (EAS) AF: 0.0145 AC: 75 AN: 5172

South Asian (SAS) AF: 0.0315 AC: 152 AN: 4818

European-Finnish (FIN) AF: 0.127 AC: 1340 AN: 10522

Middle Eastern (MID) AF: 0.0442 AC: 13 AN: 294

European-Non Finnish (NFE) AF: 0.0830 AC: 5643 AN: 67988

Other (OTH) AF: 0.0996 AC: 210 AN: 2108

Alfa AF: 0.107 Hom.: 139

Bravo AF: 0.111

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	-0.90
CADD	Benign	2.4
DANN	Benign	0.52
PhyloP100		-0.46
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: rs1535133; hg19: chr1-184437434;