Genetic Variant FAM81B:c.*156C>T (chr5-95450438-C-T) – ACMG Classification: Benign (-12 pts)

Variant summary

Our verdict is Benign. Variant got -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

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 made for transcript

Verdict is Benign. Variant got -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

Gnomad4 AFR exome

AF:

0.456

Gnomad4 AMR exome

AF:

0.176

Gnomad4 ASJ exome

AF:

0.314

Gnomad4 EAS exome

AF:

0.140

Gnomad4 SAS exome

AF:

0.242

Gnomad4 FIN exome

AF:

0.107

Gnomad4 NFE exome

AF:

0.132

Gnomad4 OTH exome

AF:

0.175

GnomAD4 genome

AF:

0.232

AC:

35231

AN:

151822

Hom.:

5491

Cov.:

AF XY:

0.232

AC XY:

17198

AN XY:

74188

show subpopulations

Gnomad4 AFR

AF:

0.441

Gnomad4 AMR

AF:

0.191

Gnomad4 ASJ

AF:

0.305

Gnomad4 EAS

AF:

0.119

Gnomad4 SAS

AF:

0.233

Gnomad4 FIN

AF:

0.0975

Gnomad4 NFE

AF:

0.141

Gnomad4 OTH

AF:

0.229

Alfa

AF:

0.176

Hom.:

1058

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

DANN

Benign

0.53

Splicing

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

Computational scores

Splicing

Publications

LitVar

Other links and lift over