dbSNP rs2536163: FAM3C:c.382+41G>A (chr7-121362856-C-T) – ACMG Classification: Benign (-12 pts)

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_014888.3(FAM3C):c.382+41G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.2 in 1,124,474 control chromosomes in the GnomAD database, including 25,614 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 0.25 ( 5872 hom., cov: 32)

Exomes 𝑓: 0.19 ( 19742 hom. )

Consequence

FAM3C
NM_014888.3 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.378

Publications

7 publications found

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]

FAM3C links:

Genome browser will be placed here

ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -12 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.7).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.429 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
FAM3C	NM_014888.3 link	c.382+41G>A		intron_variant	Intron 7 of 9	ENST00000359943.8	NP_055703.1	Q92520

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
FAM3C	ENST00000359943.8 link	c.382+41G>A		intron_variant	Intron 7 of 9	1	NM_014888.3	ENSP00000353025.3		Q92520

Frequencies

GnomAD3 genomes

AF:

0.254

AC:

38632

AN:

151920

Hom.:

5855

Cov.:

show subpopulations

Gnomad AFR

AF:

0.434

Gnomad AMI

AF:

0.192

Gnomad AMR

AF:

0.174

Gnomad ASJ

AF:

0.154

Gnomad EAS

AF:

0.0406

Gnomad SAS

AF:

0.211

Gnomad FIN

AF:

0.187

Gnomad MID

AF:

0.193

Gnomad NFE

AF:

0.200

Gnomad OTH

AF:

0.232

GnomAD2 exomes

AF:

0.192

AC:

45212

AN:

235748

AF XY:

0.189

show subpopulations

Gnomad AFR exome

AF:

0.425

Gnomad AMR exome

AF:

0.159

Gnomad ASJ exome

AF:

0.155

Gnomad EAS exome

AF:

0.0450

Gnomad FIN exome

AF:

0.184

Gnomad NFE exome

AF:

0.195

Gnomad OTH exome

AF:

0.179

GnomAD4 exome

AF:

0.192

AC:

186465

AN:

972436

Hom.:

19742

Cov.:

AF XY:

0.192

AC XY:

96732

AN XY:

504560

show subpopulations

African (AFR)

AF:

0.429

AC:

9975

AN:

23228

American (AMR)

AF:

0.160

AC:

6509

AN:

40644

Ashkenazi Jewish (ASJ)

AF:

0.158

AC:

3622

AN:

22944

East Asian (EAS)

AF:

0.0285

AC:

1046

AN:

36662

South Asian (SAS)

AF:

0.202

AC:

14729

AN:

73082

European-Finnish (FIN)

AF:

0.187

AC:

9910

AN:

53110

Middle Eastern (MID)

AF:

0.201

AC:

971

AN:

4834

European-Non Finnish (NFE)

AF:

0.195

AC:

131135

AN:

673894

Other (OTH)

AF:

0.195

AC:

8568

AN:

44038

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.487

Heterozygous variant carriers

6735

13470

20205

26940

33675

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

3394

6788

10182

13576

16970

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

GnomAD4 genome

AF:

0.254

AC:

38689

AN:

152038

Hom.:

5872

Cov.:

AF XY:

0.250

AC XY:

18564

AN XY:

74318

show subpopulations

African (AFR)

AF:

0.434

AC:

18012

AN:

41466

American (AMR)

AF:

0.173

AC:

2649

AN:

15274

Ashkenazi Jewish (ASJ)

AF:

0.154

AC:

533

AN:

3470

East Asian (EAS)

AF:

0.0405

AC:

210

AN:

5180

South Asian (SAS)

AF:

0.211

AC:

1016

AN:

4820

European-Finnish (FIN)

AF:

0.187

AC:

1974

AN:

10558

Middle Eastern (MID)

AF:

0.194

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.200

AC:

13579

AN:

67956

Other (OTH)

AF:

0.230

AC:

484

AN:

2108

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.501

Heterozygous variant carriers

1366

2731

4097

5462

6828

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

386

772

1158

1544

1930

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

Alfa

AF:

0.231

Hom.:

1153

Bravo

AF:

0.259

Asia WGS

AF:

0.139

AC:

480

AN:

3470

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.70

CADD

Benign

(source)

DANN

Benign

0.81

PhyloP100

-0.38

RBP_binding_hub_radar

0.0

RBP_regulation_power_radar

1.0

Mutation Taster

=100/0

polymorphism (auto)

(source)

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

You must be logged in to view publications. This limit was set because tens of millions (!) of queries from AI bots are generated daily.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over