rs388972

Variant summary

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

The NM_198215.4(FAM13C):​c.443+5639C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.405 in 151,632 control chromosomes in the GnomAD database, including 12,684 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 0.40 ( 12684 hom., cov: 31)

Consequence

FAM13C
NM_198215.4 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.615
Variant links:
Genes affected
FAM13C (HGNC:19371): (family with sequence similarity 13 member C)

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.88).
BA1
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.49 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
FAM13CNM_198215.4 linkuse as main transcriptc.443+5639C>T intron_variant ENST00000618804.5

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
FAM13CENST00000618804.5 linkuse as main transcriptc.443+5639C>T intron_variant 1 NM_198215.4 A1Q8NE31-1

Frequencies

GnomAD3 genomes
AF:
0.405
AC:
61324
AN:
151514
Hom.:
12677
Cov.:
31
show subpopulations
Gnomad AFR
AF:
0.496
Gnomad AMI
AF:
0.363
Gnomad AMR
AF:
0.374
Gnomad ASJ
AF:
0.359
Gnomad EAS
AF:
0.472
Gnomad SAS
AF:
0.409
Gnomad FIN
AF:
0.357
Gnomad MID
AF:
0.369
Gnomad NFE
AF:
0.362
Gnomad OTH
AF:
0.386
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.405
AC:
61361
AN:
151632
Hom.:
12684
Cov.:
31
AF XY:
0.404
AC XY:
29942
AN XY:
74090
show subpopulations
Gnomad4 AFR
AF:
0.495
Gnomad4 AMR
AF:
0.373
Gnomad4 ASJ
AF:
0.359
Gnomad4 EAS
AF:
0.472
Gnomad4 SAS
AF:
0.409
Gnomad4 FIN
AF:
0.357
Gnomad4 NFE
AF:
0.362
Gnomad4 OTH
AF:
0.384
Alfa
AF:
0.379
Hom.:
2039
Bravo
AF:
0.411
Asia WGS
AF:
0.439
AC:
1524
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.88
CADD
Benign
1.4
DANN
Benign
0.75

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: rs388972; hg19: chr10-61078109; API