rs1803389

Variant names:

• chr7-121349625-A-T
• rs1803389
• NM_014888.3:c.*836T>A

Variant summary

Our verdict is Benign. The variant received -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
• 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=-0.69).
• 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 rank	MANE	Protein	UniProt
FAM3C	NM_014888.3	c.*836T>A		3_prime_UTR_variant	Exon 10 of 10	ENST00000359943.8	NP_055703.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
FAM3C	ENST00000359943.8	c.*836T>A		3_prime_UTR_variant	Exon 10 of 10	1	NM_014888.3	ENSP00000353025.3
FAM3C	ENST00000850865.1	c.*836T>A		3_prime_UTR_variant	Exon 10 of 10			ENSP00000520951.1

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

African (AFR) AC: 0 AN: 0

American (AMR) AC: 0 AN: 0

Ashkenazi Jewish (ASJ) AC: 0 AN: 0

East Asian (EAS) AC: 0 AN: 0

South Asian (SAS) AC: 0 AN: 0

European-Finnish (FIN) AF: 0.125 AC: 28 AN: 224

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 2

European-Non Finnish (NFE) AC: 0 AN: 0

Other (OTH) AF: 0.00 AC: 0 AN: 2

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

African (AFR) AF: 0.0388 AC: 1610 AN: 41526

American (AMR) AF: 0.120 AC: 1832 AN: 15262

Ashkenazi Jewish (ASJ) AF: 0.132 AC: 457 AN: 3470

East Asian (EAS) AF: 0.00174 AC: 9 AN: 5184

South Asian (SAS) AF: 0.0587 AC: 282 AN: 4802

European-Finnish (FIN) AF: 0.171 AC: 1805 AN: 10570

Middle Eastern (MID) AF: 0.119 AC: 35 AN: 294

European-Non Finnish (NFE) AF: 0.178 AC: 12071 AN: 67858

Other (OTH) AF: 0.124 AC: 261 AN: 2110

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
PhyloP100		-0.10
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: rs1803389; hg19: chr7-120989679;