rs1803389

Positions:

• chr7-121349625-A-T

Variant summary

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

The NM_014888.3(FAM3C):​c.*836T>A variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.122 in 152,214 control chromosomes in the GnomAD database, including 990 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 0.12 (989 hom., cov: 30)
  • Exomes 𝑓: 0.12 (1 hom.)
• Consequence: FAM3C NM_014888.3 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.105

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=-0.69).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.175 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
FAM3C	NM_014888.3	c.*836T>A		3_prime_UTR_variant	10/10	ENST00000359943.8

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
FAM3C	ENST00000359943.8	c.*836T>A		3_prime_UTR_variant	10/10	1	NM_014888.3	P1

Frequencies

GnomAD3 genomes AF: 0.122 AC: 18520 AN: 151868 Hom.: 989 Cov.: 30

Gnomad AFR AF: 0.0386

Gnomad AMI AF: 0.184

Gnomad AMR AF: 0.120

Gnomad ASJ AF: 0.132

Gnomad EAS AF: 0.00173

Gnomad SAS AF: 0.0583

Gnomad FIN AF: 0.171

Gnomad MID AF: 0.123

Gnomad NFE AF: 0.178

Gnomad OTH AF: 0.125

GnomAD4 exome AF: 0.123 AC: 28 AN: 228 Hom.: 1 Cov.: 0 AF XY: 0.109 AC XY: 14 AN XY: 128

Gnomad4 FIN exome AF: 0.125

Gnomad4 OTH exome AF: 0.00

GnomAD4 genome AF: 0.122 AC: 18529 AN: 151986 Hom.: 989 Cov.: 30 AF XY: 0.120 AC XY: 8950 AN XY: 74328

Gnomad4 AFR AF: 0.0388

Gnomad4 AMR AF: 0.120

Gnomad4 ASJ AF: 0.132

Gnomad4 EAS AF: 0.00174

Gnomad4 SAS AF: 0.0587

Gnomad4 FIN AF: 0.171

Gnomad4 NFE AF: 0.178

Gnomad4 OTH AF: 0.124

Alfa AF: 0.163 Hom.: 188

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.69
CADD	Benign	7.7
DANN	Benign	0.89

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: rs1803389; hg19: chr7-120989679;