rs1990446

Positions:

• chr7-121370155-T-C

Variant summary

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

The NM_014888.3(FAM3C):​c.272+1145A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.256 in 152,140 control chromosomes in the GnomAD database, including 5,963 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 0.26 (5963 hom., cov: 32)
• Consequence: FAM3C NM_014888.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.704

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=-0.89).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.433 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
FAM3C	NM_014888.3	c.272+1145A>G		intron_variant		ENST00000359943.8	NP_055703.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
FAM3C	ENST00000359943.8	c.272+1145A>G		intron_variant		1	NM_014888.3	ENSP00000353025.3
FAM3C	ENST00000412653.5	c.272+1145A>G		intron_variant		4		ENSP00000408636.1
FAM3C	ENST00000426156.1	c.182+1145A>G		intron_variant		5		ENSP00000414940.1

Frequencies

GnomAD3 genomes AF: 0.255 AC: 38828 AN: 152022 Hom.: 5937 Cov.: 32

Gnomad AFR AF: 0.438

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: 0.233

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

GnomAD4 genome AF: 0.256 AC: 38894 AN: 152140 Hom.: 5963 Cov.: 32 AF XY: 0.251 AC XY: 18661 AN XY: 74396

Gnomad4 AFR AF: 0.438

Gnomad4 AMR AF: 0.174

Gnomad4 ASJ AF: 0.154

Gnomad4 EAS AF: 0.0405

Gnomad4 SAS AF: 0.211

Gnomad4 FIN AF: 0.187

Gnomad4 NFE AF: 0.200

Gnomad4 OTH AF: 0.230

Alfa AF: 0.228 Hom.: 1148

Bravo AF: 0.260

Asia WGS AF: 0.142 AC: 492 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	1.2
DANN	Benign	0.40

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: rs1990446; hg19: chr7-121010209;