7-121359967-AT-ATT

Position:

• chr7-121359967-AT-ATT

Variant summary

Our verdict is Benign. Variant got -8 ACMG points: 0P and 8B. BA1

The ENST00000359943.8(FAM3C):​c.467+75_467+76insA variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.413 in 750,732 control chromosomes in the GnomAD database, including 57,360 homozygotes. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency:
  • Genomes: 𝑓 0.54 (24493 hom., cov: 0)
  • Exomes 𝑓: 0.38 (32867 hom.)
• Consequence: FAM3C ENST00000359943.8 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.455

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 -8 ACMG points.

• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.801 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
FAM3C	NM_014888.3	c.467+75_467+76insA		intron_variant		ENST00000359943.8	NP_055703.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
FAM3C	ENST00000359943.8	c.467+75_467+76insA		intron_variant		1	NM_014888.3	ENSP00000353025	P1

Frequencies

GnomAD3 genomes AF: 0.544 AC: 81914 AN: 150660 Hom.: 24455 Cov.: 0

Gnomad AFR AF: 0.808

Gnomad AMI AF: 0.391

Gnomad AMR AF: 0.432

Gnomad ASJ AF: 0.468

Gnomad EAS AF: 0.166

Gnomad SAS AF: 0.425

Gnomad FIN AF: 0.409

Gnomad MID AF: 0.462

Gnomad NFE AF: 0.473

Gnomad OTH AF: 0.516

GnomAD4 exome AF: 0.380 AC: 227776 AN: 599964 Hom.: 32867 AF XY: 0.381 AC XY: 123175 AN XY: 323692

Gnomad4 AFR exome AF: 0.678

Gnomad4 AMR exome AF: 0.336

Gnomad4 ASJ exome AF: 0.400

Gnomad4 EAS exome AF: 0.144

Gnomad4 SAS exome AF: 0.369

Gnomad4 FIN exome AF: 0.377

Gnomad4 NFE exome AF: 0.394

Gnomad4 OTH exome AF: 0.400

GnomAD4 genome AF: 0.544 AC: 82001 AN: 150768 Hom.: 24493 Cov.: 0 AF XY: 0.532 AC XY: 39183 AN XY: 73606

Gnomad4 AFR AF: 0.808

Gnomad4 AMR AF: 0.432

Gnomad4 ASJ AF: 0.468

Gnomad4 EAS AF: 0.165

Gnomad4 SAS AF: 0.424

Gnomad4 FIN AF: 0.409

Gnomad4 NFE AF: 0.473

Gnomad4 OTH AF: 0.518

Bravo AF: 0.559

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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: rs3837124; hg19: chr7-121000021;