rs4338740

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_152647.3(FAM227B):​c.1012+65111A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.22 in 151,566 control chromosomes in the GnomAD database, including 4,019 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 0.22 ( 4019 hom., cov: 32)

Consequence

FAM227B
NM_152647.3 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -1.46
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]

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.98).
BA1
GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.322 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE Protein UniProt
FAM227BNM_152647.3 linkuse as main transcriptc.1012+65111A>G intron_variant ENST00000299338.11 NP_689860.2 Q96M60-1
FGF7NM_002009.4 linkuse as main transcriptc.286+18517T>C intron_variant ENST00000267843.9 NP_002000.1 P21781-1A0A7U3JVY2

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Protein Appris UniProt
FAM227BENST00000299338.11 linkuse as main transcriptc.1012+65111A>G intron_variant 2 NM_152647.3 ENSP00000299338.6 Q96M60-1
FGF7ENST00000267843.9 linkuse as main transcriptc.286+18517T>C intron_variant 1 NM_002009.4 ENSP00000267843.4 P21781-1

Frequencies

GnomAD3 genomes
AF:
0.220
AC:
33305
AN:
151448
Hom.:
4018
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.132
Gnomad AMI
AF:
0.227
Gnomad AMR
AF:
0.201
Gnomad ASJ
AF:
0.276
Gnomad EAS
AF:
0.0854
Gnomad SAS
AF:
0.337
Gnomad FIN
AF:
0.309
Gnomad MID
AF:
0.256
Gnomad NFE
AF:
0.263
Gnomad OTH
AF:
0.230
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.220
AC:
33318
AN:
151566
Hom.:
4019
Cov.:
32
AF XY:
0.224
AC XY:
16601
AN XY:
74024
show subpopulations
Gnomad4 AFR
AF:
0.132
Gnomad4 AMR
AF:
0.201
Gnomad4 ASJ
AF:
0.276
Gnomad4 EAS
AF:
0.0858
Gnomad4 SAS
AF:
0.336
Gnomad4 FIN
AF:
0.309
Gnomad4 NFE
AF:
0.263
Gnomad4 OTH
AF:
0.227
Alfa
AF:
0.257
Hom.:
8404
Bravo
AF:
0.204
Asia WGS
AF:
0.212
AC:
738
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.98
CADD
Benign
0.25
DANN
Benign
0.73

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

LitVar

Below is the list of publications found by LitVar. It may be empty.

Other links and lift over

dbSNP: rs4338740; hg19: chr15-49735297; API