NM_152647.3:c.1012+39983C>A

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_152647.3(FAM227B):​c.1012+39983C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.324 in 151,934 control chromosomes in the GnomAD database, including 8,720 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 0.32 ( 8720 hom., cov: 32)

Consequence

FAM227B
NM_152647.3 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.308

Publications

1 publications found
Variant links:
Genes affected
FAM227B (HGNC:26543): (family with sequence similarity 227 member B)
FGF7 (HGNC:3685): (fibroblast growth factor 7) The protein encoded by this gene is a member of the fibroblast growth factor (FGF) family. FGF family members possess broad mitogenic and cell survival activities, and are involved in a variety of biological processes, including embryonic development, cell growth, morphogenesis, tissue repair, tumor growth and invasion. This protein is a potent epithelial cell-specific growth factor, whose mitogenic activity is predominantly exhibited in keratinocytes but not in fibroblasts and endothelial cells. Studies of mouse and rat homologs of this gene implicated roles in morphogenesis of epithelium, reepithelialization of wounds, hair development and early lung organogenesis. [provided by RefSeq, Jul 2008]

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=-0.82).
BA1
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.447 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
FAM227BNM_152647.3 linkc.1012+39983C>A intron_variant Intron 11 of 15 ENST00000299338.11 NP_689860.2 Q96M60-1
FGF7NM_002009.4 linkc.287-14923G>T intron_variant Intron 2 of 3 ENST00000267843.9 NP_002000.1 P21781-1A0A7U3JVY2

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
FAM227BENST00000299338.11 linkc.1012+39983C>A intron_variant Intron 11 of 15 2 NM_152647.3 ENSP00000299338.6 Q96M60-1
FGF7ENST00000267843.9 linkc.287-14923G>T intron_variant Intron 2 of 3 1 NM_002009.4 ENSP00000267843.4 P21781-1

Frequencies

GnomAD3 genomes
AF:
0.324
AC:
49231
AN:
151816
Hom.:
8708
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.452
Gnomad AMI
AF:
0.180
Gnomad AMR
AF:
0.377
Gnomad ASJ
AF:
0.217
Gnomad EAS
AF:
0.382
Gnomad SAS
AF:
0.278
Gnomad FIN
AF:
0.244
Gnomad MID
AF:
0.341
Gnomad NFE
AF:
0.253
Gnomad OTH
AF:
0.320
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.324
AC:
49289
AN:
151934
Hom.:
8720
Cov.:
32
AF XY:
0.323
AC XY:
23966
AN XY:
74256
show subpopulations
African (AFR)
AF:
0.452
AC:
18743
AN:
41452
American (AMR)
AF:
0.376
AC:
5737
AN:
15238
Ashkenazi Jewish (ASJ)
AF:
0.217
AC:
752
AN:
3470
East Asian (EAS)
AF:
0.381
AC:
1974
AN:
5178
South Asian (SAS)
AF:
0.280
AC:
1351
AN:
4818
European-Finnish (FIN)
AF:
0.244
AC:
2567
AN:
10524
Middle Eastern (MID)
AF:
0.360
AC:
105
AN:
292
European-Non Finnish (NFE)
AF:
0.253
AC:
17218
AN:
67942
Other (OTH)
AF:
0.322
AC:
678
AN:
2108
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.502
Heterozygous variant carriers
0
1633
3266
4899
6532
8165
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance

Age Distribution

Genome Het
Genome Hom
Variant carriers
0
482
964
1446
1928
2410
<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:
0.288
Hom.:
843
Bravo
AF:
0.343
Asia WGS
AF:
0.326
AC:
1132
AN:
3470

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.82
CADD
Benign
1.9
DANN
Benign
0.43
PhyloP100
-0.31
Mutation Taster
=100/0
polymorphism (auto)

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

Other links and lift over

dbSNP: rs2413959; hg19: chr15-49760425; API