rs369910414

Variant names:

• chr17-81544015-C-A
• NM_025161.6:c.2416G>T

Your query was ambiguous. Multiple possible variants found:

• chr17-81544015-C-A
• chr17-81544015-C-T

Variant summary

Our verdict is Uncertain significance. Variant got 2 ACMG points: 2P and 0B. PM2

The NM_025161.6(FAAP100):​c.2416G>T​(p.Gly806Trp) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000548 in 1,459,734 control chromosomes in the GnomAD database, with no homozygous occurrence. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar. Another variant affecting the same amino acid position, but resulting in a different missense (i.e. G806R) has been classified as Uncertain significance.

• Frequency:
  • Genomes: not found (cov: 34)
  • Exomes 𝑓: 0.0000055 (0 hom.)
• Consequence: FAAP100 NM_025161.6 missense
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.539

Genes affected

FAAP100 (HGNC:26171): (FA core complex associated protein 100) FAAP100 is a component of the Fanconi anemia (FA; MIM 277650) core complex and is required for core complex stability and FANCD2 (see MIM 227646) monoubiquitination (Ling et al., 2007 [PubMed 17396147]).[supplied by OMIM, Mar 2008]

ACMG classification

Verdict is Uncertain_significance. Variant got 2 ACMG points.

• PM2: Very rare variant in population databases, with high coverage

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
FAAP100	NM_025161.6	c.2416G>T	p.Gly806Trp	missense_variant	Exon 7 of 9	ENST00000327787.13	NP_079437.5
FAAP100	XM_006722111.3	c.2002G>T	p.Gly668Trp	missense_variant	Exon 7 of 9		XP_006722174.1
FAAP100	XM_047436848.1	c.1963G>T	p.Gly655Trp	missense_variant	Exon 6 of 8		XP_047292804.1
FAAP100	NR_033338.2	n.2635G>T		non_coding_transcript_exon_variant	Exon 7 of 9

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
FAAP100	ENST00000327787.13	c.2416G>T	p.Gly806Trp	missense_variant	Exon 7 of 9	1	NM_025161.6	ENSP00000333283.8

Frequencies

GnomAD3 genomes Cov.: 34

GnomAD4 exome AF: 0.00000548 AC: 8 AN: 1459734 Hom.: 0 Cov.: 30 AF XY: 0.00000689 AC XY: 5 AN XY: 726166

Gnomad4 AFR exome AF: 0.00

Gnomad4 AMR exome AF: 0.00

Gnomad4 ASJ exome AF: 0.00

Gnomad4 EAS exome AF: 0.00

Gnomad4 SAS exome AF: 0.00

Gnomad4 FIN exome AF: 0.00

Gnomad4 NFE exome AF: 0.00000720

Gnomad4 OTH exome AF: 0.00

GnomAD4 genome Cov.: 34

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Benign	0.27
BayesDel_addAF	Benign	-0.14	T
BayesDel_noAF	Benign	-0.44
CADD	Benign	16
DANN	Uncertain	0.99
DEOGEN2	Benign	0.13	T;.
Eigen	Benign	-0.46
Eigen_PC	Benign	-0.73
FATHMM_MKL	Benign	0.083	N
LIST_S2	Benign	0.83	T;T
M_CAP	Uncertain	0.096	D
MetaRNN	Uncertain	0.52	D;D
MetaSVM	Benign	-1.0	T
MutationAssessor	Uncertain	2.2	M;.
PROVEAN	Uncertain	-3.4	D;D
REVEL	Benign	0.072
Sift	Uncertain	0.024	D;D
Sift4G	Uncertain	0.054	T;D
Polyphen		1.0	D;D
Vest4		0.55
MutPred		0.42		Gain of MoRF binding (P = 0.0312);.;
MVP		0.25
MPC		1.2
ClinPred		0.98	D
GERP RS		-4.6
RBP_binding_hub_radar		0.0
RBP_regulation_power_radar		1.1
Varity_R		0.20
gMVP		0.29

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

No publications associated with this variant yet.

Other links and lift over

hg19: chr17-79511041; COSMIC: COSV100585317;