7-121393137-A-G

Position:

• chr7-121393137-A-G

Variant summary

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

The NM_014888.3(FAM3C):​c.-42+3025T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.508 in 151,950 control chromosomes in the GnomAD database, including 20,828 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 0.51 (20828 hom., cov: 31)
• Consequence: FAM3C NM_014888.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.322

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=-0.95).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.685 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
FAM3C	NM_014888.3	c.-42+3025T>C		intron_variant		ENST00000359943.8	NP_055703.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
FAM3C	ENST00000359943.8	c.-42+3025T>C		intron_variant		1	NM_014888.3	ENSP00000353025	P1
FAM3C	ENST00000412653.5	c.-42+3162T>C		intron_variant		4		ENSP00000408636
FAM3C	ENST00000426156.1	c.-188+3025T>C		intron_variant		5		ENSP00000414940

Frequencies

GnomAD3 genomes AF: 0.508 AC: 77059 AN: 151832 Hom.: 20789 Cov.: 31

Gnomad AFR AF: 0.691

Gnomad AMI AF: 0.390

Gnomad AMR AF: 0.419

Gnomad ASJ AF: 0.465

Gnomad EAS AF: 0.167

Gnomad SAS AF: 0.426

Gnomad FIN AF: 0.406

Gnomad MID AF: 0.459

Gnomad NFE AF: 0.468

Gnomad OTH AF: 0.494

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

GnomAD4 genome AF: 0.508 AC: 77150 AN: 151950 Hom.: 20828 Cov.: 31 AF XY: 0.497 AC XY: 36898 AN XY: 74238

Gnomad4 AFR AF: 0.691

Gnomad4 AMR AF: 0.418

Gnomad4 ASJ AF: 0.465

Gnomad4 EAS AF: 0.167

Gnomad4 SAS AF: 0.425

Gnomad4 FIN AF: 0.406

Gnomad4 NFE AF: 0.468

Gnomad4 OTH AF: 0.496

Alfa AF: 0.517 Hom.: 3715

Bravo AF: 0.518

Asia WGS AF: 0.362 AC: 1260 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	1.3
DANN	Benign	0.38

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: rs7793554; hg19: chr7-121033191;