Genetic Variant FAM187B:p.Trp188* (chr19-35228117-C-T) – ACMG Classification: Benign (-8 pts)

Variant summary

Our verdict is Benign. The variant received -8 ACMG points: 0P and 8B. BA1

The NM_152481.2(FAM187B):c.564G>A(p.Trp188*) variant causes a stop gained change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.331 in 1,614,010 control chromosomes in the GnomAD database, including 90,628 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. Variant results in nonsense mediated mRNA decay.

Frequency

Genomes: 𝑓 0.33 ( 8275 hom., cov: 33)

Exomes 𝑓: 0.33 ( 82353 hom. )

Consequence

FAM187B
NM_152481.2 stop_gained

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.718

Publications

39 publications found

Variant links:

Genes affected

FAM187B (HGNC:26366): (family with sequence similarity 187 member B) Predicted to be integral component of membrane. [provided by Alliance of Genome Resources, Apr 2022]

FAM187B links:

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ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -8 ACMG points.

BA1

GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.44 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_152481.2. 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
	FAM187B	NM_152481.2	MANE Select	c.564G>A	p.Trp188*	stop_gained	Exon 1 of 2	NP_689694.1	Q17R55

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	FAM187B	ENST00000324675.4	TSL:1 MANE Select	c.564G>A	p.Trp188*	stop_gained	Exon 1 of 2	ENSP00000323355.3	Q17R55

Frequencies

GnomAD3 genomes

AF:

0.328

AC:

49848

AN:

152046

Hom.:

8276

Cov.:

show subpopulations

Gnomad AFR

AF:

0.309

Gnomad AMI

AF:

0.377

Gnomad AMR

AF:

0.343

Gnomad ASJ

AF:

0.338

Gnomad EAS

AF:

0.174

Gnomad SAS

AF:

0.458

Gnomad FIN

AF:

0.335

Gnomad MID

AF:

0.411

Gnomad NFE

AF:

0.334

Gnomad OTH

AF:

0.362

GnomAD2 exomes

AF:

0.336

AC:

84450

AN:

251222

AF XY:

0.344

show subpopulations

Gnomad AFR exome

AF:

0.308

Gnomad AMR exome

AF:

0.337

Gnomad ASJ exome

AF:

0.329

Gnomad EAS exome

AF:

0.177

Gnomad FIN exome

AF:

0.337

Gnomad NFE exome

AF:

0.330

Gnomad OTH exome

AF:

0.339

GnomAD4 exome

AF:

0.331

AC:

484374

AN:

1461846

Hom.:

82353

Cov.:

AF XY:

0.335

AC XY:

243907

AN XY:

727210

show subpopulations

African (AFR)

AF:

0.301

AC:

10078

AN:

33480

American (AMR)

AF:

0.341

AC:

15253

AN:

44720

Ashkenazi Jewish (ASJ)

AF:

0.343

AC:

8953

AN:

26136

East Asian (EAS)

AF:

0.152

AC:

6022

AN:

39700

South Asian (SAS)

AF:

0.466

AC:

40220

AN:

86258

European-Finnish (FIN)

AF:

0.329

AC:

17581

AN:

53412

Middle Eastern (MID)

AF:

0.424

AC:

2445

AN:

5766

European-Non Finnish (NFE)

AF:

0.327

AC:

363066

AN:

1111978

Other (OTH)

AF:

0.344

AC:

20756

AN:

60396

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.475

Heterozygous variant carriers

22733

45466

68199

90932

113665

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

11790

23580

35370

47160

58950

<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:

0.328

AC:

49879

AN:

152164

Hom.:

8275

Cov.:

AF XY:

0.330

AC XY:

24540

AN XY:

74374

show subpopulations

African (AFR)

AF:

0.309

AC:

12843

AN:

41514

American (AMR)

AF:

0.344

AC:

5253

AN:

15284

Ashkenazi Jewish (ASJ)

AF:

0.338

AC:

1173

AN:

3470

East Asian (EAS)

AF:

0.174

AC:

901

AN:

5178

South Asian (SAS)

AF:

0.456

AC:

2203

AN:

4830

European-Finnish (FIN)

AF:

0.335

AC:

3549

AN:

10590

Middle Eastern (MID)

AF:

0.414

AC:

121

AN:

292

European-Non Finnish (NFE)

AF:

0.334

AC:

22734

AN:

67990

Other (OTH)

AF:

0.360

AC:

759

AN:

2106

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.497

Heterozygous variant carriers

1781

3563

5344

7126

8907

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

506

1012

1518

2024

2530

<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:

0.332

Hom.:

14911

Bravo

AF:

0.322

TwinsUK

AF:

0.322

AC:

1194

ALSPAC

AF:

0.331

AC:

1276

ESP6500AA

AF:

0.320

AC:

1409

ESP6500EA

AF:

0.328

AC:

2823

ExAC

AF:

0.337

AC:

40920

Asia WGS

AF:

0.352

AC:

1223

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

BayesDel_addAF

Benign

-0.075

BayesDel_noAF

Pathogenic

0.26

CADD

Pathogenic

(source)

DANN

Benign

0.97

Eigen

Benign

0.13

Eigen_PC

Benign

-0.25

FATHMM_MKL

Benign

0.088

PhyloP100

0.72

Vest4

0.073

GERP RS

1.2

Mutation Taster

=185/15

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