rs708017

Variant summary

Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong

The NM_173558.4(FGD2):​c.*834C>A variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. 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: 28)

Consequence

FGD2
NM_173558.4 3_prime_UTR

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.771
Variant links:
Genes affected
FGD2 (HGNC:3664): (FYVE, RhoGEF and PH domain containing 2) The protein encoded by this gene belongs to a family of guanine nucleotide exchange factors (GEFs) which control cytoskeleton-dependent membrane rearrangements by activating the cell division cycle 42 (CDC42) protein. This gene is expressed in B lymphocytes, macrophages, and dendritic cells. The encoded protein may play a role in leukocyte signaling and vesicle trafficking in antigen-presenting cells in the immune system. [provided by RefSeq, Oct 2016]

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ACMG classification

Classification made for transcript

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=-0.89).

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
FGD2NM_173558.4 linkc.*834C>A 3_prime_UTR_variant Exon 16 of 16 ENST00000274963.13 NP_775829.2 Q7Z6J4-1
FGD2XM_047418333.1 linkc.*834C>A 3_prime_UTR_variant Exon 13 of 13 XP_047274289.1
FGD2XM_047418334.1 linkc.*834C>A 3_prime_UTR_variant Exon 11 of 11 XP_047274290.1
FGD2XM_047418335.1 linkc.*834C>A 3_prime_UTR_variant Exon 9 of 9 XP_047274291.1

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
FGD2ENST00000274963.13 linkc.*834C>A 3_prime_UTR_variant Exon 16 of 16 1 NM_173558.4 ENSP00000274963.8 Q7Z6J4-1
FGD2ENST00000487920.1 linkn.2545C>A non_coding_transcript_exon_variant Exon 3 of 3 2
FGD2ENST00000494343.5 linkn.2859C>A non_coding_transcript_exon_variant Exon 12 of 12 5

Frequencies

GnomAD3 genomes
Cov.:
28
GnomAD4 exome
Cov.:
0
GnomAD4 genome
Cov.:
28

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.89
CADD
Benign
0.71
DANN
Benign
0.32

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

Below is the list of publications found by LitVar. It may be empty.

Other links and lift over

dbSNP: rs708017; hg19: chr6-36996773; API