chr10-101770141-TAAAAAAA-T

Variant summary

Our verdict is Likely benign. Variant got -4 ACMG points: 0P and 4B. BS2

The NM_033163.5(FGF8):​c.*181_*187delTTTTTTT variant causes a 3 prime UTR change. The variant allele was found at a frequency of 0.000022 in 272,286 control chromosomes in the GnomAD database, with no homozygous occurrence. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: not found (cov: 0)
Exomes 𝑓: 0.000022 ( 0 hom. )

Consequence

FGF8
NM_033163.5 3_prime_UTR

Scores

Not classified

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 4.86
Variant links:
Genes affected
FGF8 (HGNC:3686): (fibroblast growth factor 8) 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 known to be a factor that supports androgen and anchorage independent growth of mammary tumor cells. Overexpression of this gene has been shown to increase tumor growth and angiogensis. The adult expression of this gene is restricted to testes and ovaries. Temporal and spatial pattern of this gene expression suggests its function as an embryonic epithelial factor. Studies of the mouse and chick homologs revealed roles in midbrain and limb development, organogenesis, embryo gastrulation and left-right axis determination. The alternative splicing of this gene results in four transcript variants. [provided by RefSeq, Jul 2008]

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ACMG classification

Classification made for transcript

Verdict is Likely_benign. Variant got -4 ACMG points.

BS2
High AC in GnomAdExome4 at 6 AD,Digenic gene.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
FGF8NM_033163.5 linkc.*181_*187delTTTTTTT 3_prime_UTR_variant Exon 6 of 6 ENST00000320185.7 NP_149353.1 P55075-4A1A515

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
FGF8ENST00000320185 linkc.*181_*187delTTTTTTT 3_prime_UTR_variant Exon 6 of 6 1 NM_033163.5 ENSP00000321797.2 P55075-4
FGF8ENST00000344255 linkc.*181_*187delTTTTTTT 3_prime_UTR_variant Exon 6 of 6 1 ENSP00000340039.3 P55075-1
FGF8ENST00000469792.6 linkn.*880_*886delTTTTTTT splice_region_variant, non_coding_transcript_exon_variant Exon 5 of 5 5 ENSP00000473299.1 R4GMQ3
FGF8ENST00000469792.6 linkn.*880_*886delTTTTTTT 3_prime_UTR_variant Exon 5 of 5 5 ENSP00000473299.1 R4GMQ3

Frequencies

GnomAD3 genomes
Cov.:
0
GnomAD4 exome
AF:
0.0000220
AC:
6
AN:
272286
Hom.:
0
AF XY:
0.0000143
AC XY:
2
AN XY:
139812
show subpopulations
Gnomad4 AFR exome
AF:
0.000133
Gnomad4 AMR exome
AF:
0.00
Gnomad4 ASJ exome
AF:
0.00
Gnomad4 EAS exome
AF:
0.00
Gnomad4 SAS exome
AF:
0.000132
Gnomad4 FIN exome
AF:
0.00
Gnomad4 NFE exome
AF:
0.0000117
Gnomad4 OTH exome
AF:
0.0000601
GnomAD4 genome
Cov.:
0

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction

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.

Other links and lift over

dbSNP: rs11322844; hg19: chr10-103529898; API