Genetic Variant NM_152548.3:c.*156C>T (chr5-95450438-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 NM_152548.3(FAM81B):c.*156C>T variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.16 in 1,265,342 control chromosomes in the GnomAD database, including 20,343 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 0.23 ( 5491 hom., cov: 32)

Exomes 𝑓: 0.15 ( 14852 hom. )

Consequence

FAM81B
NM_152548.3 3_prime_UTR

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.379

Publications

5 publications found

Variant links:

Genes affected

FAM81B (HGNC:26335): (family with sequence similarity 81 member B) Located in nucleus. [provided by Alliance of Genome Resources, Apr 2022]

FAM81B 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=-0.89).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.435 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	Effect	Exon rank	MANE	Protein	UniProt
FAM81B	NM_152548.3 link	c.*156C>T	3_prime_UTR_variant	Exon 10 of 10	ENST00000283357.10	NP_689761.2	Q96LP2
FAM81B	XM_011543209.2 link	c.*156C>T	3_prime_UTR_variant	Exon 8 of 8		XP_011541511.1
FAM81B	XM_011543210.3 link	c.*156C>T	3_prime_UTR_variant	Exon 7 of 7		XP_011541512.1
FAM81B	XM_047416823.1 link	c.*156C>T	3_prime_UTR_variant	Exon 7 of 7		XP_047272779.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
FAM81B	ENST00000283357.10 link	c.*156C>T		3_prime_UTR_variant	Exon 10 of 10	1	NM_152548.3	ENSP00000283357.5		Q96LP2

Frequencies

GnomAD3 genomes

AF:

0.232

AC:

35183

AN:

151704

Hom.:

5471

Cov.:

show subpopulations

Gnomad AFR

AF:

0.440

Gnomad AMI

AF:

0.109

Gnomad AMR

AF:

0.191

Gnomad ASJ

AF:

0.305

Gnomad EAS

AF:

0.119

Gnomad SAS

AF:

0.234

Gnomad FIN

AF:

0.0975

Gnomad MID

AF:

0.297

Gnomad NFE

AF:

0.141

Gnomad OTH

AF:

0.232

GnomAD4 exome

AF:

0.150

AC:

167205

AN:

1113520

Hom.:

14852

Cov.:

AF XY:

0.154

AC XY:

85109

AN XY:

554442

show subpopulations

African (AFR)

AF:

0.456

AC:

10313

AN:

22606

American (AMR)

AF:

0.176

AC:

2782

AN:

15776

Ashkenazi Jewish (ASJ)

AF:

0.314

AC:

6176

AN:

19690

East Asian (EAS)

AF:

0.140

AC:

4188

AN:

29828

South Asian (SAS)

AF:

0.242

AC:

14416

AN:

59548

European-Finnish (FIN)

AF:

0.107

AC:

4303

AN:

40336

Middle Eastern (MID)

AF:

0.319

AC:

1288

AN:

4042

European-Non Finnish (NFE)

AF:

0.132

AC:

115620

AN:

875190

Other (OTH)

AF:

0.175

AC:

8119

AN:

46504

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.508

Heterozygous variant carriers

6484

12969

19453

25938

32422

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

4204

8408

12612

16816

21020

<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:

0.232

AC:

35231

AN:

151822

Hom.:

5491

Cov.:

AF XY:

0.232

AC XY:

17198

AN XY:

74188

show subpopulations

African (AFR)

AF:

0.441

AC:

18224

AN:

41362

American (AMR)

AF:

0.191

AC:

2912

AN:

15260

Ashkenazi Jewish (ASJ)

AF:

0.305

AC:

1056

AN:

3466

East Asian (EAS)

AF:

0.119

AC:

618

AN:

5182

South Asian (SAS)

AF:

0.233

AC:

1123

AN:

4812

European-Finnish (FIN)

AF:

0.0975

AC:

1023

AN:

10494

Middle Eastern (MID)

AF:

0.286

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.141

AC:

9609

AN:

67936

Other (OTH)

AF:

0.229

AC:

483

AN:

2108

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.504

Heterozygous variant carriers

1256

2512

3768

5024

6280

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

354

708

1062

1416

1770

<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:

0.188

Hom.:

1343

Bravo

AF:

0.246

Asia WGS

AF:

0.142

AC:

494

AN:

3470

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.89

CADD

Benign

2.0

(source)

DANN

Benign

0.53

PhyloP100

-0.38

Mutation Taster

=100/0

polymorphism (auto)

(source)

Splicing

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

Transcripts

RefSeq

Ensembl

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over