chr1-162378847-C-T

Position:

• chr1-162378847-C-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_001135240.3(C1orf226):​c.-67C>T variant causes a 5 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.161 in 954,828 control chromosomes in the GnomAD database, including 13,297 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 (1790 hom., cov: 32)
  • Exomes 𝑓: 0.16 (11507 hom.)
• Consequence: C1orf226 NM_001135240.3 5_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.487

Genes affected

C1orf226 (HGNC:34351): (chromosome 1 open reading frame 226)

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.177 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
C1orf226	NM_001135240.3	c.-67C>T		5_prime_UTR_variant	1/3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
C1orf226	ENST00000426197.2	c.-67C>T		5_prime_UTR_variant	1/3	2		A2

Frequencies

GnomAD3 genomes AF: 0.147 AC: 22336 AN: 152032 Hom.: 1787 Cov.: 32

Gnomad AFR AF: 0.0880

Gnomad AMI AF: 0.141

Gnomad AMR AF: 0.137

Gnomad ASJ AF: 0.260

Gnomad EAS AF: 0.0636

Gnomad SAS AF: 0.142

Gnomad FIN AF: 0.175

Gnomad MID AF: 0.297

Gnomad NFE AF: 0.180

Gnomad OTH AF: 0.184

GnomAD4 exome AF: 0.164 AC: 131384 AN: 802678 Hom.: 11507 Cov.: 10 AF XY: 0.164 AC XY: 66423 AN XY: 405564

Gnomad4 AFR exome AF: 0.0910

Gnomad4 AMR exome AF: 0.113

Gnomad4 ASJ exome AF: 0.250

Gnomad4 EAS exome AF: 0.0932

Gnomad4 SAS exome AF: 0.144

Gnomad4 FIN exome AF: 0.171

Gnomad4 NFE exome AF: 0.169

Gnomad4 OTH exome AF: 0.172

GnomAD4 genome AF: 0.147 AC: 22346 AN: 152150 Hom.: 1790 Cov.: 32 AF XY: 0.146 AC XY: 10852 AN XY: 74360

Gnomad4 AFR AF: 0.0879

Gnomad4 AMR AF: 0.137

Gnomad4 ASJ AF: 0.260

Gnomad4 EAS AF: 0.0633

Gnomad4 SAS AF: 0.144

Gnomad4 FIN AF: 0.175

Gnomad4 NFE AF: 0.180

Gnomad4 OTH AF: 0.185

Alfa AF: 0.172 Hom.: 3152

Bravo AF: 0.140

Asia WGS AF: 0.120 AC: 415 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	1.6
DANN	Benign	0.79

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: rs164187; hg19: chr1-162348637; COSMIC: COSV63397054; COSMIC: COSV63397054;