GeneBe

rs3078330

Variant names:

Variant summary

Our verdict is Uncertain significance. Variant got 2 ACMG points: 2P and 0B. PM2

The NM_198215.4(FAM13C):​c.-50_-49dupTA variant causes a 5 prime UTR change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: not found (cov: 32)

Consequence

FAM13C
NM_198215.4 5_prime_UTR

Scores

Not classified

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.147
Variant links:
Genes affected
FAM13C (HGNC:19371): (family with sequence similarity 13 member C)

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ACMG classification

Classification made for transcript

Verdict is Uncertain_significance. Variant got 2 ACMG points.

PM2
Very rare variant in population databases, with high coverage;

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
FAM13CNM_198215.4 linkc.-50_-49dupTA 5_prime_UTR_variant Exon 1 of 14 ENST00000618804.5 NP_937858.2 Q8NE31-1A8K181

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
FAM13CENST00000618804.5 linkc.-50_-49dupTA 5_prime_UTR_variant Exon 1 of 14 1 NM_198215.4 ENSP00000481854.1 Q8NE31-1

Frequencies

GnomAD3 genomes
Cov.:
32
GnomAD3 exomes
AF:
0.999
AC:
233026
AN:
233246
Hom.:
116404
AF XY:
0.999
AC XY:
125411
AN XY:
125500
show subpopulations
Gnomad AFR exome
AF:
0.987
Gnomad AMR exome
AF:
0.999
Gnomad ASJ exome
AF:
1.00
Gnomad EAS exome
AF:
1.00
Gnomad SAS exome
AF:
1.00
Gnomad FIN exome
AF:
1.00
Gnomad NFE exome
AF:
1.00
Gnomad OTH exome
AF:
1.00
GnomAD4 exome
Cov.:
31
GnomAD4 genome
Cov.:
32
Alfa
AF:
0.492
Hom.:
6760
Asia WGS
AF:
0.999
AC:
3475
AN:
3478

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: rs3078330; hg19: chr10-61122268; API