19-39872380-G-C

Variant names:

• chr19-39872380-G-C
• rs741143
• ENST00000616721.6:c.11447C>G

Variant summary

Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2 BP4_Strong

The NM_003890.3(FCGBP):​c.11486C>G​(p.Ala3829Gly) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000338 in 1,213,346 control chromosomes in the GnomAD database, with no homozygous occurrence. 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: not found (cov: 33)
  • Exomes 𝑓: 0.000034 (0 hom.)
• Consequence: FCGBP NM_003890.3 missense
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.818

Genes affected

FCGBP (HGNC:13572): (Fc gamma binding protein) Located in extracellular exosome. [provided by Alliance of Genome Resources, Apr 2022]

ACMG classification

Verdict is Likely_benign. Variant got -2 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.47).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
FCGBP	NM_003890.3	c.11486C>G	p.Ala3829Gly	missense_variant	Exon 32 of 36		NP_003881.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
FCGBP	ENST00000616721.6	c.11447C>G	p.Ala3816Gly	missense_variant	Exon 24 of 28	1		ENSP00000481056.3

Frequencies

GnomAD3 genomes Cov.: 33

GnomAD3 exomes AF: 0.000128 AC: 31 AN: 241416 Hom.: 0 AF XY: 0.000122 AC XY: 16 AN XY: 131680

Gnomad AFR exome AF: 0.000199

Gnomad AMR exome AF: 0.0000295

Gnomad ASJ exome AF: 0.000101

Gnomad EAS exome AF: 0.000623

Gnomad SAS exome AF: 0.0000986

Gnomad FIN exome AF: 0.0000959

Gnomad NFE exome AF: 0.0000836

Gnomad OTH exome AF: 0.000169

GnomAD4 exome AF: 0.0000338 AC: 41 AN: 1213346 Hom.: 0 Cov.: 33 AF XY: 0.0000482 AC XY: 29 AN XY: 601292

Gnomad4 AFR exome AF: 0.0000761

Gnomad4 AMR exome AF: 0.00

Gnomad4 ASJ exome AF: 0.00

Gnomad4 EAS exome AF: 0.00144

Gnomad4 SAS exome AF: 0.00

Gnomad4 FIN exome AF: 0.0000312

Gnomad4 NFE exome AF: 0.0000147

Gnomad4 OTH exome AF: 0.00

GnomAD4 genome Cov.: 33

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.47
CADD	Benign	11
DANN	Uncertain	0.98

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: rs741143; hg19: chr19-40363020;