Variant 12-13055618-C-T details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -13 ACMG points: 0P and 13B. BP4_ModerateBP6_ModerateBP7BA1

The NM_020853.2(FAM234B):c.105C>T(p.Asp35=) 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 (★).

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 criteria provided, single submitter B:1

Conservation

PhyloP100: 0.123

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:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -13 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 id is 3060079.Status of the report is criteria_provided_single_submitter, 1 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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
FAM234B	NM_020853.2 linkuse as main transcript	c.105C>T	p.Asp35=	synonymous_variant	2/13	ENST00000197268.13

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
FAM234B	ENST00000197268.13 linkuse as main transcript	c.105C>T	p.Asp35=	synonymous_variant	2/13	1	NM_020853.2	P1
FAM234B	ENST00000416494.6 linkuse as main transcript	c.105C>T	p.Asp35=	synonymous_variant, NMD_transcript_variant	2/14	2

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

GnomAD3 exomes

AF:

0.245

AC:

61543

AN:

251330

Hom.:

9489

AF XY:

0.236

AC XY:

32067

AN XY:

135846

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 SAS exome

AF:

0.274

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

Gnomad4 AFR exome

AF:

0.357

Gnomad4 AMR exome

AF:

0.355

Gnomad4 ASJ exome

AF:

0.236

Gnomad4 EAS exome

AF:

0.488

Gnomad4 SAS exome

AF:

0.270

Gnomad4 FIN exome

AF:

0.209

Gnomad4 NFE exome

AF:

0.138

Gnomad4 OTH exome

AF:

0.194

GnomAD4 genome

AF:

0.237

AC:

36034

AN:

152064

Hom.:

5195

Cov.:

AF XY:

0.243

AC XY:

18041

AN XY:

74322

show subpopulations

Gnomad4 AFR

AF:

0.354

Gnomad4 AMR

AF:

0.239

Gnomad4 ASJ

AF:

0.223

Gnomad4 EAS

AF:

0.526

Gnomad4 SAS

AF:

0.280

Gnomad4 FIN

AF:

0.223

Gnomad4 NFE

AF:

0.142

Gnomad4 OTH

AF:

0.226

Alfa

AF:

0.176

Hom.:

3597

Bravo

AF:

0.249

Asia WGS

AF:

0.422

AC:

1467

AN:

3478

EpiCase

AF:

0.146

EpiControl

AF:

0.147

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

LINK: link

Submissions by phenotype

FAM234B-related disorder

Benign:1

Benign, criteria provided, single submitter

clinical testing

PreventionGenetics, part of Exact Sciences

Oct 21, 2019

This variant is classified as benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications). -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.45

Cadd

Benign

5.5

Dann

Benign

0.33

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

Submissions by phenotype

Computational scores

Splicing

Publications

LitVar

Other links and lift over