Genetic Variant FAM234B:p.Asp35Asp (chr12-13055618-C-T) – ACMG Classification: Benign (-12 pts)

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_ModerateBP6BP7BA1

The NM_020853.2(FAM234B):c.105C>T(p.Asp35Asp) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.18 in 1,613,744 control chromosomes in the GnomAD database, including 32,431 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (no stars).

Frequency

Genomes: 𝑓 0.24 ( 5195 hom., cov: 32)

Exomes 𝑓: 0.17 ( 27236 hom. )

Consequence

FAM234B
NM_020853.2 synonymous

Scores

Clinical Significance

Benign no assertion criteria provided B:1

Conservation

PhyloP100: 0.123

Publications

19 publications found

Variant links:

Genes affected

FAM234B (HGNC:29288): (family with sequence similarity 234 member B) Predicted to be located in Golgi apparatus and cytoskeleton. Predicted to be integral component of membrane. [provided by Alliance of Genome Resources, Apr 2022]

FAM234B links:

Genome browser will be placed here

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=-0.45).

BP6

Variant 12-13055618-C-T is Benign according to our data. Variant chr12-13055618-C-T is described in ClinVar as Benign. ClinVar VariationId is 3060079.Status of the report is no_assertion_criteria_provided, 0 stars.

BP7

Synonymous conserved (PhyloP=0.123 with no splicing effect.

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.51 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_020853.2. 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
	FAM234B	NM_020853.2	MANE Select	c.105C>T	p.Asp35Asp	synonymous	Exon 2 of 13	NP_065904.1	A2RU67

Ensembl Transcripts

Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
FAM234B	ENST00000197268.13	TSL:1 MANE Select	c.105C>T	p.Asp35Asp	synonymous	Exon 2 of 13	ENSP00000197268.8	A2RU67
FAM234B	ENST00000893327.1		c.105C>T	p.Asp35Asp	synonymous	Exon 2 of 12	ENSP00000563386.1
FAM234B	ENST00000416494.6	TSL:2	n.105C>T		non_coding_transcript_exon	Exon 2 of 14	ENSP00000394063.2	A2RU67

Frequencies

GnomAD3 genomes

AF:

0.237

AC:

35953

AN:

151946

Hom.:

5170

Cov.:

show subpopulations

Gnomad AFR

AF:

0.354

Gnomad AMI

AF:

0.300

Gnomad AMR

AF:

0.238

Gnomad ASJ

AF:

0.223

Gnomad EAS

AF:

0.525

Gnomad SAS

AF:

0.280

Gnomad FIN

AF:

0.223

Gnomad MID

AF:

0.206

Gnomad NFE

AF:

0.142

Gnomad OTH

AF:

0.225

GnomAD2 exomes

AF:

0.245

AC:

61543

AN:

251330

AF XY:

0.236

show subpopulations

Gnomad AFR exome

AF:

0.362

Gnomad AMR exome

AF:

0.375

Gnomad ASJ exome

AF:

0.233

Gnomad EAS exome

AF:

0.527

Gnomad FIN exome

AF:

0.213

Gnomad NFE exome

AF:

0.144

Gnomad OTH exome

AF:

0.209

GnomAD4 exome

AF:

0.174

AC:

253903

AN:

1461680

Hom.:

27236

Cov.:

AF XY:

0.176

AC XY:

127622

AN XY:

727108

show subpopulations

African (AFR)

AF:

0.357

AC:

11933

AN:

33472

American (AMR)

AF:

0.355

AC:

15891

AN:

44718

Ashkenazi Jewish (ASJ)

AF:

0.236

AC:

6170

AN:

26132

East Asian (EAS)

AF:

0.488

AC:

19374

AN:

39696

South Asian (SAS)

AF:

0.270

AC:

23251

AN:

86254

European-Finnish (FIN)

AF:

0.209

AC:

11164

AN:

53404

Middle Eastern (MID)

AF:

0.205

AC:

1180

AN:

5768

European-Non Finnish (NFE)

AF:

0.138

AC:

153230

AN:

1111844

Other (OTH)

AF:

0.194

AC:

11710

AN:

60392

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.480

Heterozygous variant carriers

11030

22061

33091

44122

55152

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

6008

12016

18024

24032

30040

<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:

0.237

AC:

36034

AN:

152064

Hom.:

5195

Cov.:

AF XY:

0.243

AC XY:

18041

AN XY:

74322

show subpopulations

African (AFR)

AF:

0.354

AC:

14692

AN:

41450

American (AMR)

AF:

0.239

AC:

3660

AN:

15282

Ashkenazi Jewish (ASJ)

AF:

0.223

AC:

775

AN:

3472

East Asian (EAS)

AF:

0.526

AC:

2719

AN:

5168

South Asian (SAS)

AF:

0.280

AC:

1347

AN:

4814

European-Finnish (FIN)

AF:

0.223

AC:

2361

AN:

10572

Middle Eastern (MID)

AF:

0.204

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.142

AC:

9670

AN:

67988

Other (OTH)

AF:

0.226

AC:

477

AN:

2114

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.502

Heterozygous variant carriers

1324

2647

3971

5294

6618

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

376

752

1128

1504

1880

<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:

0.182

Hom.:

4722

Bravo

AF:

0.249

Asia WGS

AF:

0.422

AC:

1467

AN:

3478

EpiCase

AF:

0.146

EpiControl

AF:

0.147

ClinVar

ClinVar submissions

Significance:Benign

Revision:no assertion criteria provided

View on ClinVar

Pathogenic

VUS

Benign

Condition

FAM234B-related disorder (1)

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.45

CADD

Benign

5.5

(source)

DANN

Benign

0.33

PhyloP100

0.12

Mutation Taster

=100/0

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

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