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GeneBe

13-32155568-G-A

Variant summary

Our verdict is Benign. Variant got -15 ACMG points: 0P and 15B. BP4_StrongBP6_ModerateBP7BS1BS2

The NM_023037.3(FRY):c.1557G>A(p.Pro519=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00123 in 1,612,496 control chromosomes in the GnomAD database, including 13 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

Frequency

Genomes: 𝑓 0.0063 ( 8 hom., cov: 32)
Exomes 𝑓: 0.00071 ( 5 hom. )

Consequence

FRY
NM_023037.3 synonymous

Scores

2

Clinical Significance

Benign criteria provided, single submitter B:1

Conservation

PhyloP100: -3.31
Variant links:
Genes affected
FRY (HGNC:20367): (FRY microtubule binding protein) Predicted to enable enzyme inhibitor activity. Predicted to be involved in cell morphogenesis and neuron projection development. Predicted to be located in microtubule organizing center and spindle pole. Predicted to be active in cell cortex and site of polarized growth. [provided by Alliance of Genome Resources, Apr 2022]

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -15 ACMG points.

BP4
?
    BP4 - Multiple lines of computational evidence suggest no impact on gene or gene product (conservation, evolutionary, splicing impact, etc.)
Computational evidence support a benign effect (BayesDel_noAF=-0.81).
BP6
?
    BP6 - Reputable source recently reports variant as benign, but the evidence is not available to the laboratory to perform an independent evaluation
Variant 13-32155568-G-A is Benign according to our data. Variant chr13-32155568-G-A is described in ClinVar as [Benign]. Clinvar id is 719505.Status of the report is criteria_provided_single_submitter, 1 stars.
BP7
?
    BP7 - A synonymous (silent) variant for which splicing prediction algorithms predict no impact to the splice consensus sequence nor the creation of a new splice site AND the nucleotide is not highly conserved
Synonymous conserved (PhyloP=-3.31 with no splicing effect.
BS1
?
    BS1 - Allele frequency is greater than expected for disorder
Variant frequency is greater than expected in population afr. gnomad4 allele frequency = 0.00627 (954/152266) while in subpopulation AFR AF= 0.0214 (888/41560). AF 95% confidence interval is 0.0202. There are 8 homozygotes in gnomad4. There are 463 alleles in male gnomad4 subpopulation. Median coverage is 32. This position pass quality control queck.
BS2
?
    BS2 - Observed in a healthy adult individual for a recessive (homozygous), dominant (heterozygous), or X-linked (hemizygous) disorder, with full penetrance expected at an early age
High AC in GnomAd at 955 AD gene.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
FRYNM_023037.3 linkuse as main transcriptc.1557G>A p.Pro519= synonymous_variant 15/61 ENST00000542859.6

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
FRYENST00000542859.6 linkuse as main transcriptc.1557G>A p.Pro519= synonymous_variant 15/615 NM_023037.3 A1
FRYENST00000647500.1 linkuse as main transcriptc.1692G>A p.Pro564= synonymous_variant 15/61
FRYENST00000642040.1 linkuse as main transcriptc.1557G>A p.Pro519= synonymous_variant 15/62 P4
FRYENST00000645780.1 linkuse as main transcriptc.1407G>A p.Pro469= synonymous_variant 16/62

Frequencies

GnomAD3 genomes
?
    Genome Aggregation Database, over 76,156 genomes
AF:
0.00628
AC:
955
AN:
152148
Hom.:
8
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.0215
Gnomad AMI
AF:
0.00
Gnomad AMR
AF:
0.00255
Gnomad ASJ
AF:
0.00
Gnomad EAS
AF:
0.00
Gnomad SAS
AF:
0.000207
Gnomad FIN
AF:
0.00
Gnomad MID
AF:
0.00
Gnomad NFE
AF:
0.000221
Gnomad OTH
AF:
0.00526
GnomAD3 exomes
AF:
0.00160
AC:
398
AN:
249346
Hom.:
3
AF XY:
0.00131
AC XY:
177
AN XY:
135282
show subpopulations
Gnomad AFR exome
AF:
0.0203
Gnomad AMR exome
AF:
0.00113
Gnomad ASJ exome
AF:
0.000298
Gnomad EAS exome
AF:
0.00
Gnomad SAS exome
AF:
0.00
Gnomad FIN exome
AF:
0.00
Gnomad NFE exome
AF:
0.000283
Gnomad OTH exome
AF:
0.00165
GnomAD4 exome
AF:
0.000708
AC:
1034
AN:
1460230
Hom.:
5
Cov.:
29
AF XY:
0.000637
AC XY:
463
AN XY:
726484
show subpopulations
Gnomad4 AFR exome
AF:
0.0189
Gnomad4 AMR exome
AF:
0.00132
Gnomad4 ASJ exome
AF:
0.000115
Gnomad4 EAS exome
AF:
0.00
Gnomad4 SAS exome
AF:
0.0000464
Gnomad4 FIN exome
AF:
0.00
Gnomad4 NFE exome
AF:
0.000222
Gnomad4 OTH exome
AF:
0.00146
GnomAD4 genome
?
    Genome Aggregation Database, over 76,156 genomes
AF:
0.00627
AC:
954
AN:
152266
Hom.:
8
Cov.:
32
AF XY:
0.00622
AC XY:
463
AN XY:
74454
show subpopulations
Gnomad4 AFR
AF:
0.0214
Gnomad4 AMR
AF:
0.00255
Gnomad4 ASJ
AF:
0.00
Gnomad4 EAS
AF:
0.00
Gnomad4 SAS
AF:
0.000207
Gnomad4 FIN
AF:
0.00
Gnomad4 NFE
AF:
0.000221
Gnomad4 OTH
AF:
0.00521
Alfa
AF:
0.00137
Hom.:
5
Bravo
AF:
0.00729
EpiCase
AF:
0.000218
EpiControl
AF:
0.000771

ClinVar

Significance: Benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link

Submissions by phenotype

not provided Benign:1
Benign, criteria provided, single submitterclinical testingInvitaeDec 31, 2019- -

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.81
Cadd
Benign
0.029
Dann
Benign
0.70

Splicing

Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
0.010
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: rs116121141; hg19: chr13-32729705; API