dbSNP rs350402: ENSG00000254706:c.-11-3044C>T (chr1-162378847-C-T) – ACMG Classification: Benign (-12 pts)

Variant summary

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

The ENST00000420220.1(ENSG00000254706):c.-11-3044C>T variant causes a intron 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

ENSG00000254706
ENST00000420220.1 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.487

Publications

7 publications found

Variant links:

Genes affected

ENSG00000254706 (HGNC:):

ENSG00000254706 links:

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

C1orf226 links:

Genome browser will be placed here

new If you want to explore the variant's impact on the transcript ENST00000420220.1, 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=-0.92).

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.177 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000420220.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	C1orf226	NM_001135240.4		c.-196C>T		upstream_gene	N/A	NP_001128712.2	A1L170-1

Ensembl Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein	UniProt
ENSG00000254706	ENST00000420220.1	TSL:5	c.-11-3044C>T	intron	N/A	ENSP00000398035.1	F8W6W0
C1orf226	ENST00000426197.2	TSL:2	c.-67C>T	5_prime_UTR	Exon 1 of 3	ENSP00000413150.2	A1L170-2
ENSG00000254706	ENST00000431696.1	TSL:4	c.227-3044C>T	intron	N/A	ENSP00000405676.2	H7C2G1

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

African (AFR)

AF:

0.0910

AC:

1712

AN:

18804

American (AMR)

AF:

0.113

AC:

2711

AN:

24030

Ashkenazi Jewish (ASJ)

AF:

0.250

AC:

4417

AN:

17666

East Asian (EAS)

AF:

0.0932

AC:

2814

AN:

30182

South Asian (SAS)

AF:

0.144

AC:

7670

AN:

53296

European-Finnish (FIN)

AF:

0.171

AC:

7701

AN:

44950

Middle Eastern (MID)

AF:

0.303

AC:

796

AN:

2630

European-Non Finnish (NFE)

AF:

0.169

AC:

97298

AN:

574762

Other (OTH)

AF:

0.172

AC:

6265

AN:

36358

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.502

Heterozygous variant carriers

5422

10844

16266

21688

27110

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

2798

5596

8394

11192

13990

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

GnomAD4 genome

AF:

0.147

AC:

22346

AN:

152150

Hom.:

1790

Cov.:

AF XY:

0.146

AC XY:

10852

AN XY:

74360

show subpopulations

African (AFR)

AF:

0.0879

AC:

3648

AN:

41520

American (AMR)

AF:

0.137

AC:

2093

AN:

15292

Ashkenazi Jewish (ASJ)

AF:

0.260

AC:

902

AN:

3470

East Asian (EAS)

AF:

0.0633

AC:

327

AN:

5162

South Asian (SAS)

AF:

0.144

AC:

692

AN:

4812

European-Finnish (FIN)

AF:

0.175

AC:

1849

AN:

10592

Middle Eastern (MID)

AF:

0.306

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.180

AC:

12226

AN:

67984

Other (OTH)

AF:

0.185

AC:

391

AN:

2114

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.502

Heterozygous variant carriers

992

1984

2976

3968

4960

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

254

508

762

1016

1270

<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:

0.170

Hom.:

3889

Bravo

AF:

0.140

Asia WGS

AF:

0.120

AC:

415

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.92

CADD

Benign

1.6

(source)

DANN

Benign

0.79

PhyloP100

-0.49

PromoterAI

-0.0060

Neutral

(source)

Mutation Taster

=299/1

polymorphism (auto)

(source)

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

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

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over