dbSNP rs10494266: C1orf54:c.46+286A>G (chr1-150273149-A-G) – ACMG Classification: Benign (-12 pts)

Variant summary

Our verdict is . The variant received -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_024579.4(C1orf54):c.46+286A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.119 in 152,206 control chromosomes in the GnomAD database, including 1,343 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as (no stars).

Frequency

Genomes: 𝑓 0.12 ( 1343 hom., cov: 32)

Consequence

C1orf54
NM_024579.4 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.0790

Publications

13 publications found

Variant links:

Genes affected

C1orf54 (HGNC:26258): (chromosome 1 open reading frame 54) Predicted to be located in extracellular region. [provided by Alliance of Genome Resources, Apr 2022]

C1orf54 links:

LOC124904414 (HGNC:):

LOC124904414 links:

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new If you want to explore the variant's impact on the transcript NM_024579.4, check out the Mutation Effect Viewer. This is especially useful for frameshift variants or if you want to visualize the effect of exon loss / intron retention.

ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -12 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.85).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.334 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_024579.4. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein	UniProt
C1orf54	NM_024579.4	MANE Select	c.46+286A>G	intron	N/A	NP_078855.2	Q8WWF1
C1orf54	NM_001301039.1		c.46+286A>G	intron	N/A	NP_001287968.1
C1orf54	NM_001301040.1		c.46+286A>G	intron	N/A	NP_001287969.1	Q8WWF1

Ensembl Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein	UniProt
C1orf54	ENST00000369099.8	TSL:1 MANE Select	c.46+286A>G	intron	N/A	ENSP00000358095.3	Q8WWF1
C1orf54	ENST00000369098.3	TSL:1	c.46+286A>G	intron	N/A	ENSP00000358094.3	Q5TB16
C1orf54	ENST00000877303.1		c.46+286A>G	intron	N/A	ENSP00000547362.1

Frequencies

GnomAD3 genomes

AF:

0.119

AC:

18137

AN:

152090

Hom.:

1344

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0596

Gnomad AMI

AF:

0.132

Gnomad AMR

AF:

0.122

Gnomad ASJ

AF:

0.119

Gnomad EAS

AF:

0.348

Gnomad SAS

AF:

0.153

Gnomad FIN

AF:

0.178

Gnomad MID

AF:

0.161

Gnomad NFE

AF:

0.125

Gnomad OTH

AF:

0.145

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome

AF:

0.119

AC:

18135

AN:

152206

Hom.:

1343

Cov.:

AF XY:

0.124

AC XY:

9258

AN XY:

74416

show subpopulations

African (AFR)

AF:

0.0597

AC:

2480

AN:

41544

American (AMR)

AF:

0.122

AC:

1869

AN:

15288

Ashkenazi Jewish (ASJ)

AF:

0.119

AC:

413

AN:

3468

East Asian (EAS)

AF:

0.347

AC:

1794

AN:

5166

South Asian (SAS)

AF:

0.153

AC:

736

AN:

4822

European-Finnish (FIN)

AF:

0.178

AC:

1879

AN:

10584

Middle Eastern (MID)

AF:

0.153

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.125

AC:

8489

AN:

68016

Other (OTH)

AF:

0.147

AC:

310

AN:

2112

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.503

Heterozygous variant carriers

817

1634

2450

3267

4084

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

214

428

642

856

1070

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

Alfa

AF:

0.125

Hom.:

1754

Bravo

AF:

0.115

Asia WGS

AF:

0.244

AC:

844

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.85

CADD

Benign

4.4

(source)

DANN

Benign

0.71

PhyloP100

-0.079

PromoterAI

-0.011

Neutral

(source)

Mutation Taster

=100/0

polymorphism (auto)

(source)

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.10

Details are displayed if max score is > 0.2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Publications

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Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Variant Effect in Transcripts

RefSeq Transcripts

Ensembl Transcripts

Frequencies

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over