7-121348703-C-T

Variant names:

• chr7-121348703-C-T
• rs2536184
• ENST00000892185.1:c.*1758G>A

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000892185.1(FAM3C):​c.*1758G>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 0.252 in 151,744 control chromosomes in the GnomAD database, including 5,706 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 0.25 (5706 hom., cov: 31)
  • Failed GnomAD Quality Control
• Consequence: FAM3C ENST00000892185.1 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.232
• Publications: 6 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=-0.91).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.42 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000892185.1. 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.*1758G>A		downstream_gene	N/A	NP_055703.1	Q92520
	FAM3C	NM_001040020.2		c.*1758G>A		downstream_gene	N/A	NP_001035109.1	Q92520

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	FAM3C	ENST00000892185.1		c.*1758G>A		3_prime_UTR	Exon 10 of 10	ENSP00000562244.1
	FAM3C	ENST00000951274.1		c.*1758G>A		3_prime_UTR	Exon 12 of 12	ENSP00000621333.1
	FAM3C	ENST00000892186.1		c.*1758G>A		3_prime_UTR	Exon 9 of 9	ENSP00000562245.1

Frequencies

GnomAD3 genomes AF: 0.252 AC: 38139 AN: 151626 Hom.: 5683 Cov.: 31

Gnomad AFR AF: 0.425

Gnomad AMI AF: 0.192

Gnomad AMR AF: 0.173

Gnomad ASJ AF: 0.152

Gnomad EAS AF: 0.0419

Gnomad SAS AF: 0.210

Gnomad FIN AF: 0.188

Gnomad MID AF: 0.184

Gnomad NFE AF: 0.199

Gnomad OTH AF: 0.228

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

GnomAD4 genome AF: 0.252 AC: 38201 AN: 151744 Hom.: 5706 Cov.: 31 AF XY: 0.247 AC XY: 18335 AN XY: 74136

African (AFR) AF: 0.426 AC: 17621 AN: 41390

American (AMR) AF: 0.173 AC: 2632 AN: 15242

Ashkenazi Jewish (ASJ) AF: 0.152 AC: 527 AN: 3464

East Asian (EAS) AF: 0.0418 AC: 216 AN: 5166

South Asian (SAS) AF: 0.210 AC: 1013 AN: 4820

European-Finnish (FIN) AF: 0.188 AC: 1975 AN: 10504

Middle Eastern (MID) AF: 0.184 AC: 54 AN: 294

European-Non Finnish (NFE) AF: 0.199 AC: 13513 AN: 67848

Other (OTH) AF: 0.226 AC: 475 AN: 2106

Alfa AF: 0.222 Hom.: 6859

Bravo AF: 0.256

Asia WGS AF: 0.140 AC: 484 AN: 3464

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.84
DANN	Benign	0.53
PhyloP100		0.23

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Other links and lift over

dbSNP: rs2536184; hg19: chr7-120988757;