Genetic Variant FAM72A:p.Thr62Ser (chr1-206199852-G-C) – ACMG Classification: Uncertain_significance (0 pts)

Variant summary

Our verdict is Uncertain significance. The variant received 0 ACMG points: 0P and 0B.

The NM_001123168.3(FAM72A):c.185C>G(p.Thr62Ser) variant causes a missense change involving the alteration of a conserved nucleotide. Variant has been reported in ClinVar as Uncertain significance (★).

Frequency

Genomes: 𝑓 0.000022 ( 0 hom., cov: 12)

Exomes 𝑓: 0.0000033 ( 0 hom. )

Failed GnomAD Quality Control

Consequence

FAM72A
NM_001123168.3 missense

Scores

Clinical Significance

Uncertain significance criteria provided, single submitter U:1

Conservation

PhyloP100: 7.77

Publications

0 publications found

Variant links:

Genes affected

FAM72A (HGNC:24044): (family with sequence similarity 72 member A) Predicted to act upstream of or within negative regulation of brain-derived neurotrophic factor-activated receptor activity and positive regulation of apoptotic process. Located in cytosol and intracellular membrane-bounded organelle. [provided by Alliance of Genome Resources, Apr 2022]

FAM72A links:

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ACMG classification

Classification was made for transcript

Our verdict: Uncertain_significance. The variant received 0 ACMG points.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001123168.3. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
FAM72A	NM_001123168.3	MANE Select	c.185C>G	p.Thr62Ser	missense	Exon 2 of 4	NP_001116640.1	Q5TYM5-1
FAM72A	NM_001317901.2		c.185C>G	p.Thr62Ser	missense	Exon 2 of 4	NP_001304830.1	Q5TYM6
FAM72A	NM_001385240.1		c.185C>G	p.Thr62Ser	missense	Exon 4 of 6	NP_001372169.1	Q5TYM5-1

Ensembl Transcripts

Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
FAM72A	ENST00000367128.8	TSL:1 MANE Select	c.185C>G	p.Thr62Ser	missense	Exon 2 of 4	ENSP00000356096.3	Q5TYM5-1
FAM72A	ENST00000341209.9	TSL:1	c.65C>G	p.Thr22Ser	missense	Exon 2 of 4	ENSP00000340661.5	Q5TYM5-2
FAM72A	ENST00000367129.6	TSL:3	c.185C>G	p.Thr62Ser	missense	Exon 2 of 4	ENSP00000356097.2	Q5TYM6

Frequencies

GnomAD3 genomes

AF:

0.0000219

AC:

AN:

91470

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0000907

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.00

Gnomad ASJ

AF:

0.00

Gnomad EAS

AF:

0.00

Gnomad SAS

AF:

0.00

Gnomad FIN

AF:

0.00

Gnomad MID

AF:

0.00

Gnomad NFE

AF:

0.00

Gnomad OTH

AF:

0.00

GnomAD4 exome

Data not reliable, filtered out with message: AS_VQSR

AF:

0.00000327

AC:

AN:

610842

Hom.:

Cov.:

AF XY:

0.00000304

AC XY:

AN XY:

328916

show subpopulations

African (AFR)

AF:

0.000121

AC:

AN:

16544

American (AMR)

AF:

0.00

AC:

AN:

35868

Ashkenazi Jewish (ASJ)

AF:

0.00

AC:

AN:

18226

East Asian (EAS)

AF:

0.00

AC:

AN:

34722

South Asian (SAS)

AF:

0.00

AC:

AN:

62220

European-Finnish (FIN)

AF:

0.00

AC:

AN:

50268

Middle Eastern (MID)

AF:

0.00

AC:

AN:

2284

European-Non Finnish (NFE)

AF:

0.00

AC:

AN:

358924

Other (OTH)

AF:

0.00

AC:

AN:

31786

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.500

Heterozygous variant carriers

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Variant carriers

<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

Data not reliable, filtered out with message: AS_VQSR

AF:

0.0000219

AC:

AN:

91470

Hom.:

Cov.:

AF XY:

0.0000237

AC XY:

AN XY:

42206

show subpopulations

African (AFR)

AF:

0.0000907

AC:

AN:

22054

American (AMR)

AF:

0.00

AC:

AN:

7928

Ashkenazi Jewish (ASJ)

AF:

0.00

AC:

AN:

2522

East Asian (EAS)

AF:

0.00

AC:

AN:

3190

South Asian (SAS)

AF:

0.00

AC:

AN:

2150

European-Finnish (FIN)

AF:

0.00

AC:

AN:

4402

Middle Eastern (MID)

AF:

0.00

AC:

AN:

236

European-Non Finnish (NFE)

AF:

0.00

AC:

AN:

47136

Other (OTH)

AF:

0.00

AC:

AN:

1156

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.575

Heterozygous variant carriers

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Variant carriers

<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:

0.00

Hom.:

ClinVar

ClinVar submissions

Significance:Uncertain significance

Revision:criteria provided, single submitter

View on ClinVar

Pathogenic

VUS

Benign

Condition

not specified (1)

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

AlphaMissense

Uncertain

0.38

BayesDel_noAF

Uncertain

0.13

CADD

Pathogenic

(source)

DANN

Uncertain

1.0

DEOGEN2

Benign

0.028

LIST_S2

Benign

0.84

MetaRNN

Uncertain

0.44

PhyloP100

7.8

PROVEAN

Benign

-1.7

Sift

Uncertain

0.027

Sift4G

Uncertain

0.036

Vest4

0.53

gMVP

0.36

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

Variant Effect in Transcripts

RefSeq Transcripts

Ensembl Transcripts

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over