chr7-121393067-T-C

Variant names:

• chr7-121393067-T-C
• rs7776725
• NM_014888.3:c.-42+3095A>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.-42+3095A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.279 in 152,098 control chromosomes in the GnomAD database, including 6,082 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 0.28 (6082 hom., cov: 32)
• Consequence: FAM3C NM_014888.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.210
• Publications: 50 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=-0.86).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.322 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_014888.3. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	FAM3C	NM_014888.3	MANE Select	c.-42+3095A>G		intron	N/A	NP_055703.1	Q92520
	FAM3C	NM_001040020.2		c.-42+3135A>G		intron	N/A	NP_001035109.1	Q92520

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	FAM3C	ENST00000359943.8	TSL:1 MANE Select	c.-42+3095A>G		intron	N/A	ENSP00000353025.3	Q92520
	FAM3C	ENST00000892202.1		c.-241A>G		5_prime_UTR	Exon 1 of 10	ENSP00000562261.1
	FAM3C	ENST00000892193.1		c.-42+3095A>G		intron	N/A	ENSP00000562252.1

Frequencies

GnomAD3 genomes AF: 0.279 AC: 42342 AN: 151980 Hom.: 6076 Cov.: 32

Gnomad AFR AF: 0.327

Gnomad AMI AF: 0.198

Gnomad AMR AF: 0.250

Gnomad ASJ AF: 0.306

Gnomad EAS AF: 0.125

Gnomad SAS AF: 0.214

Gnomad FIN AF: 0.253

Gnomad MID AF: 0.263

Gnomad NFE AF: 0.276

Gnomad OTH AF: 0.278

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

GnomAD4 genome AF: 0.279 AC: 42364 AN: 152098 Hom.: 6082 Cov.: 32 AF XY: 0.273 AC XY: 20297 AN XY: 74366

African (AFR) AF: 0.326 AC: 13529 AN: 41448

American (AMR) AF: 0.249 AC: 3813 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.306 AC: 1063 AN: 3472

East Asian (EAS) AF: 0.125 AC: 646 AN: 5178

South Asian (SAS) AF: 0.212 AC: 1023 AN: 4820

European-Finnish (FIN) AF: 0.253 AC: 2677 AN: 10580

Middle Eastern (MID) AF: 0.279 AC: 82 AN: 294

European-Non Finnish (NFE) AF: 0.276 AC: 18756 AN: 67994

Other (OTH) AF: 0.281 AC: 594 AN: 2112

Alfa AF: 0.272 Hom.: 18742

Bravo AF: 0.284

Asia WGS AF: 0.220 AC: 767 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	2.4
DANN	Benign	0.64
PhyloP100		0.21
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: rs7776725; hg19: chr7-121033121;