rs7792993

Variant names:

• chr7-121385523-A-C
• rs7792993
• NM_014888.3:c.-41-2513T>G

Your query was ambiguous. Multiple possible variants found:

• chr7-121385523-A-C
• chr7-121385523-A-G

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 4 publications found

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

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt
FAM3C	NM_014888.3	c.-41-2513T>G		intron_variant	Intron 1 of 9	ENST00000359943.8	NP_055703.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
FAM3C	ENST00000359943.8	c.-41-2513T>G		intron_variant	Intron 1 of 9	1	NM_014888.3	ENSP00000353025.3
FAM3C	ENST00000850865.1	c.-41-2513T>G		intron_variant	Intron 1 of 9			ENSP00000520951.1
FAM3C	ENST00000412653.5	c.-41-2513T>G		intron_variant	Intron 1 of 7	4		ENSP00000408636.1
FAM3C	ENST00000426156.1	c.-187-2513T>G		intron_variant	Intron 1 of 8	5		ENSP00000414940.1

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

African (AFR) AF: 0.190 AC: 7874 AN: 41482

American (AMR) AF: 0.153 AC: 2346 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.168 AC: 580 AN: 3462

East Asian (EAS) AF: 0.0402 AC: 208 AN: 5178

South Asian (SAS) AF: 0.213 AC: 1026 AN: 4818

European-Finnish (FIN) AF: 0.195 AC: 2064 AN: 10586

Middle Eastern (MID) AF: 0.184 AC: 54 AN: 294

European-Non Finnish (NFE) AF: 0.208 AC: 14140 AN: 67978

Other (OTH) AF: 0.182 AC: 384 AN: 2110

Alfa AF: 0.206 Hom.: 574

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
PhyloP100		0.13
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs7792993; hg19: chr7-121025577;