rs2707479

Variant summary

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

The NM_014888.3(FAM3C):​c.272+3151A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.257 in 152,026 control chromosomes in the GnomAD database, including 6,041 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 0.26 ( 6041 hom., cov: 32)

Consequence

FAM3C
NM_014888.3 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -2.56
Variant links:
Genes affected
FAM3C (HGNC:18664): (FAM3 metabolism regulating signaling molecule C) This gene is a member of the family with sequence similarity 3 (FAM3) family and encodes a secreted protein with a GG domain. A change in expression of this protein has been noted in pancreatic cancer-derived cells. [provided by RefSeq, Mar 2010]

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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=-0.86).
BA1
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.437 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE Protein UniProt
FAM3CNM_014888.3 linkuse as main transcriptc.272+3151A>G intron_variant ENST00000359943.8 NP_055703.1

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Protein Appris UniProt
FAM3CENST00000359943.8 linkuse as main transcriptc.272+3151A>G intron_variant 1 NM_014888.3 ENSP00000353025 P1
FAM3CENST00000412653.5 linkuse as main transcriptc.272+3151A>G intron_variant 4 ENSP00000408636
FAM3CENST00000426156.1 linkuse as main transcriptc.182+3151A>G intron_variant 5 ENSP00000414940

Frequencies

GnomAD3 genomes
AF:
0.256
AC:
38957
AN:
151908
Hom.:
6012
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.442
Gnomad AMI
AF:
0.192
Gnomad AMR
AF:
0.174
Gnomad ASJ
AF:
0.154
Gnomad EAS
AF:
0.0405
Gnomad SAS
AF:
0.210
Gnomad FIN
AF:
0.187
Gnomad MID
AF:
0.193
Gnomad NFE
AF:
0.200
Gnomad OTH
AF:
0.234
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.257
AC:
39028
AN:
152026
Hom.:
6041
Cov.:
32
AF XY:
0.252
AC XY:
18737
AN XY:
74330
show subpopulations
Gnomad4 AFR
AF:
0.442
Gnomad4 AMR
AF:
0.174
Gnomad4 ASJ
AF:
0.154
Gnomad4 EAS
AF:
0.0404
Gnomad4 SAS
AF:
0.210
Gnomad4 FIN
AF:
0.187
Gnomad4 NFE
AF:
0.200
Gnomad4 OTH
AF:
0.232
Alfa
AF:
0.244
Hom.:
913
Bravo
AF:
0.262
Asia WGS
AF:
0.141
AC:
488
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.86
CADD
Benign
0.066
DANN
Benign
0.71

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: rs2707479; hg19: chr7-121008203; API