rs7792993

chr7-121385523-A-C

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_014888.3(FAM3C):c.-41-2513T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.19 in 152,104 control chromosomes in the GnomAD database, including 2,806 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 0.19 (2806 hom., cov: 32)
• Consequence: FAM3C NM_014888.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.131

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]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.82).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.205 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
FAM3C	NM_014888.3	c.-41-2513T>G		intron_variant		ENST00000359943.8

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
FAM3C	ENST00000359943.8	c.-41-2513T>G		intron_variant		1	NM_014888.3	P1
FAM3C	ENST00000412653.5	c.-41-2513T>G		intron_variant		4
FAM3C	ENST00000426156.1	c.-187-2513T>G		intron_variant		5

Frequencies

GnomAD3 genomes AF: 0.190 AC: 28814 AN: 151986 Hom.: 2792 Cov.: 32

Gnomad AFR AF: 0.189

Gnomad AMI AF: 0.207

Gnomad AMR AF: 0.153

Gnomad ASJ AF: 0.168

Gnomad EAS AF: 0.0403

Gnomad SAS AF: 0.212

Gnomad FIN AF: 0.195

Gnomad MID AF: 0.184

Gnomad NFE AF: 0.208

Gnomad OTH AF: 0.184

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.190 AC: 28864 AN: 152104 Hom.: 2806 Cov.: 32 AF XY: 0.188 AC XY: 13962 AN XY: 74374

Gnomad4 AFR AF: 0.190

Gnomad4 AMR AF: 0.153

Gnomad4 ASJ AF: 0.168

Gnomad4 EAS AF: 0.0402

Gnomad4 SAS AF: 0.213

Gnomad4 FIN AF: 0.195

Gnomad4 NFE AF: 0.208

Gnomad4 OTH AF: 0.182

Alfa AF: 0.206 Hom.: 558

Bravo AF: 0.184

Asia WGS AF: 0.133 AC: 462 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
Cadd	Benign	5.0
Dann	Benign	0.62

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

Other links and lift over

dbSNP: rs7792993; hg19: chr7-121025577;