chr8-55941947-A-G

Variant summary

Our verdict is Benign. Variant got -7 ACMG points: 1P and 8B. PP2BP4_StrongBS2

The NM_002350.4(LYN):​c.88A>G​(p.Thr30Ala) variant causes a missense change. The variant allele was found at a frequency of 0.0000254 in 1,613,416 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 13/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★★).

Frequency

Genomes: 𝑓 0.000092 ( 0 hom., cov: 31)
Exomes 𝑓: 0.000018 ( 0 hom. )

Consequence

LYN
NM_002350.4 missense

Scores

2
17

Clinical Significance

Uncertain significance criteria provided, multiple submitters, no conflicts U:2

Conservation

PhyloP100: 4.39
Variant links:
Genes affected
LYN (HGNC:6735): (LYN proto-oncogene, Src family tyrosine kinase) This gene encodes a tyrosine protein kinase, which maybe involved in the regulation of mast cell degranulation, and erythroid differentiation. Alternatively spliced transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Jul 2011]

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -7 ACMG points.

PP2
Missense variant in gene, where missense usually causes diseases (based on misZ statistic), LYN. . Gene score misZ 3.3381 (greater than the threshold 3.09). Trascript score misZ 3.9896 (greater than threshold 3.09). GenCC has associacion of gene with autoinflammatory disease, systemic, with vasculitis.
BP4
Computational evidence support a benign effect (MetaRNN=0.03427717).
BS2
High AC in GnomAd4 at 14 AD gene.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
LYNNM_002350.4 linkuse as main transcriptc.88A>G p.Thr30Ala missense_variant 2/13 ENST00000519728.6
LYNNM_001111097.3 linkuse as main transcriptc.69+19A>G intron_variant
LYNXM_011517529.4 linkuse as main transcriptc.-135-4501A>G intron_variant

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
LYNENST00000519728.6 linkuse as main transcriptc.88A>G p.Thr30Ala missense_variant 2/131 NM_002350.4 P4P07948-1
LYNENST00000520220.6 linkuse as main transcriptc.69+19A>G intron_variant 1 A1P07948-2
LYNENST00000520050.1 linkuse as main transcriptc.88A>G p.Thr30Ala missense_variant 2/64

Frequencies

GnomAD3 genomes
AF:
0.0000920
AC:
14
AN:
152180
Hom.:
0
Cov.:
31
show subpopulations
Gnomad AFR
AF:
0.00
Gnomad AMI
AF:
0.00548
Gnomad AMR
AF:
0.00
Gnomad ASJ
AF:
0.00
Gnomad EAS
AF:
0.00
Gnomad SAS
AF:
0.00
Gnomad FIN
AF:
0.00
Gnomad MID
AF:
0.00
Gnomad NFE
AF:
0.000132
Gnomad OTH
AF:
0.00
GnomAD3 exomes
AF:
0.0000119
AC:
3
AN:
251202
Hom.:
0
AF XY:
0.0000221
AC XY:
3
AN XY:
135798
show subpopulations
Gnomad AFR exome
AF:
0.00
Gnomad AMR exome
AF:
0.00
Gnomad ASJ exome
AF:
0.00
Gnomad EAS exome
AF:
0.00
Gnomad SAS exome
AF:
0.00
Gnomad FIN exome
AF:
0.00
Gnomad NFE exome
AF:
0.0000264
Gnomad OTH exome
AF:
0.00
GnomAD4 exome
AF:
0.0000185
AC:
27
AN:
1461236
Hom.:
0
Cov.:
30
AF XY:
0.0000110
AC XY:
8
AN XY:
726958
show subpopulations
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:
0.0000234
Gnomad4 OTH exome
AF:
0.0000166
GnomAD4 genome
AF:
0.0000920
AC:
14
AN:
152180
Hom.:
0
Cov.:
31
AF XY:
0.0000135
AC XY:
1
AN XY:
74340
show subpopulations
Gnomad4 AFR
AF:
0.00
Gnomad4 AMR
AF:
0.00
Gnomad4 ASJ
AF:
0.00
Gnomad4 EAS
AF:
0.00
Gnomad4 SAS
AF:
0.00
Gnomad4 FIN
AF:
0.00
Gnomad4 NFE
AF:
0.000132
Gnomad4 OTH
AF:
0.00
Alfa
AF:
0.000116
Hom.:
0
Bravo
AF:
0.000128
ESP6500AA
AF:
0.00
AC:
0
ESP6500EA
AF:
0.000233
AC:
2
ExAC
AF:
0.0000165
AC:
2

ClinVar

Significance: Uncertain significance
Submissions summary: Uncertain:2
Revision: criteria provided, multiple submitters, no conflicts
LINK: link

Submissions by phenotype

Inborn genetic diseases Uncertain:1
Uncertain significance, criteria provided, single submitterclinical testingAmbry GeneticsNov 17, 2022The c.88A>G (p.T30A) alteration is located in exon 2 (coding exon 1) of the LYN gene. This alteration results from a A to G substitution at nucleotide position 88, causing the threonine (T) at amino acid position 30 to be replaced by an alanine (A). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. -
not provided Uncertain:1
Uncertain significance, criteria provided, single submitterclinical testingInvitaeNov 18, 2023This sequence change replaces threonine, which is neutral and polar, with alanine, which is neutral and non-polar, at codon 30 of the LYN protein (p.Thr30Ala). This variant is present in population databases (rs377153434, gnomAD 0.004%). This variant has not been reported in the literature in individuals affected with LYN-related conditions. ClinVar contains an entry for this variant (Variation ID: 1504325). An algorithm developed to predict the effect of missense changes on protein structure and function (PolyPhen-2) suggests that this variant is likely to be tolerated. In summary, the available evidence is currently insufficient to determine the role of this variant in disease. Therefore, it has been classified as a Variant of Uncertain Significance. -

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
AlphaMissense
Benign
0.14
BayesDel_addAF
Benign
-0.090
T
BayesDel_noAF
Benign
-0.30
CADD
Benign
20
DANN
Benign
0.80
DEOGEN2
Benign
0.28
T;.
Eigen
Benign
-0.17
Eigen_PC
Benign
0.049
FATHMM_MKL
Uncertain
0.89
D
LIST_S2
Benign
0.66
T;T
M_CAP
Benign
0.016
T
MetaRNN
Benign
0.034
T;T
MetaSVM
Benign
-0.80
T
MutationAssessor
Benign
1.1
L;.
MutationTaster
Benign
0.88
D;D
PrimateAI
Uncertain
0.54
T
PROVEAN
Benign
-0.20
N;N
REVEL
Benign
0.14
Sift
Benign
0.76
T;T
Sift4G
Benign
0.85
T;T
Polyphen
0.0
B;.
Vest4
0.22
MVP
0.66
MPC
0.97
ClinPred
0.20
T
GERP RS
5.7
Varity_R
0.14
gMVP
0.53

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: rs377153434; hg19: chr8-56854506; API