Variant rs350402 details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

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

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.487

Variant links:

Genes affected

ENSG00000254706 (HGNC:):

ENSG00000254706 links:

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

C1orf226 links:

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ACMG classification

Classification made for transcript

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	Protein	UniProt
C1orf226	NM_001135240.3 linkuse as main transcript	c.-67C>T		5_prime_UTR_variant	1/3		NP_001128712.1	A1L170-2

Ensembl

Gene	Transcript	HGVSc	Effect	#exon/exons	TSL	Protein	UniProt
ENSG00000254706	ENST00000420220.1 linkuse as main transcript	c.-11-3044C>T	intron_variant		5	ENSP00000398035.1	F8W6W0
C1orf226	ENST00000426197.2 linkuse as main transcript	c.-67C>T	5_prime_UTR_variant	1/3	2	ENSP00000413150.2	A1L170-2
ENSG00000254706	ENST00000431696.1 linkuse as main transcript	c.227-3044C>T	intron_variant		4	ENSP00000405676.2	H7C2G1
ENSG00000254706	ENST00000367932.3 linkuse as main transcript	n.153-3044C>T	intron_variant		4	ENSP00000356909.3	H7BY61

Frequencies

GnomAD3 genomes

AF:

0.147

AC:

22336

AN:

152032

Hom.:

1787

Cov.:

show subpopulations

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.:

AF XY:

0.164

AC XY:

66423

AN XY:

405564

show subpopulations

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.:

AF XY:

0.146

AC XY:

10852

AN XY:

74360

show subpopulations

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

Below is the list of publications found by LitVar. It may be empty.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Computational scores

Splicing

Publications

LitVar

Other links and lift over