rs7813271
Positions:
Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_002350.4(LYN):c.383+35A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.19 in 1,581,486 control chromosomes in the GnomAD database, including 31,463 homozygotes. 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: 𝑓 0.24 ( 5166 hom., cov: 32)
Exomes 𝑓: 0.18 ( 26297 hom. )
Consequence
LYN
NM_002350.4 intron
NM_002350.4 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -0.536
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 -12 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.89).
BA1
?
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.393 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
LYN | NM_002350.4 | c.383+35A>G | intron_variant | ENST00000519728.6 | |||
LYN | NM_001111097.3 | c.320+35A>G | intron_variant | ||||
LYN | XM_011517529.4 | c.116+35A>G | intron_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
LYN | ENST00000519728.6 | c.383+35A>G | intron_variant | 1 | NM_002350.4 | P4 | |||
LYN | ENST00000520220.6 | c.320+35A>G | intron_variant | 1 | A1 | ||||
LYN | ENST00000520050.1 | c.383+35A>G | intron_variant | 4 |
Frequencies
GnomAD3 genomes ? AF: 0.236 AC: 35889AN: 151954Hom.: 5150 Cov.: 32
GnomAD3 genomes
?
AF:
AC:
35889
AN:
151954
Hom.:
Cov.:
32
Gnomad AFR
AF:
Gnomad AMI
AF:
Gnomad AMR
AF:
Gnomad ASJ
AF:
Gnomad EAS
AF:
Gnomad SAS
AF:
Gnomad FIN
AF:
Gnomad MID
AF:
Gnomad NFE
AF:
Gnomad OTH
AF:
GnomAD3 exomes AF: 0.175 AC: 43850AN: 250314Hom.: 4687 AF XY: 0.175 AC XY: 23628AN XY: 135304
GnomAD3 exomes
AF:
AC:
43850
AN:
250314
Hom.:
AF XY:
AC XY:
23628
AN XY:
135304
Gnomad AFR exome
AF:
Gnomad AMR exome
AF:
Gnomad ASJ exome
AF:
Gnomad EAS exome
AF:
Gnomad SAS exome
AF:
Gnomad FIN exome
AF:
Gnomad NFE exome
AF:
Gnomad OTH exome
AF:
GnomAD4 exome AF: 0.185 AC: 264192AN: 1429414Hom.: 26297 Cov.: 25 AF XY: 0.184 AC XY: 131418AN XY: 712950
GnomAD4 exome
AF:
AC:
264192
AN:
1429414
Hom.:
Cov.:
25
AF XY:
AC XY:
131418
AN XY:
712950
Gnomad4 AFR exome
AF:
Gnomad4 AMR exome
AF:
Gnomad4 ASJ exome
AF:
Gnomad4 EAS exome
AF:
Gnomad4 SAS exome
AF:
Gnomad4 FIN exome
AF:
Gnomad4 NFE exome
AF:
Gnomad4 OTH exome
AF:
GnomAD4 genome ? AF: 0.236 AC: 35939AN: 152072Hom.: 5166 Cov.: 32 AF XY: 0.229 AC XY: 17021AN XY: 74318
GnomAD4 genome
?
AF:
AC:
35939
AN:
152072
Hom.:
Cov.:
32
AF XY:
AC XY:
17021
AN XY:
74318
Gnomad4 AFR
AF:
Gnomad4 AMR
AF:
Gnomad4 ASJ
AF:
Gnomad4 EAS
AF:
Gnomad4 SAS
AF:
Gnomad4 FIN
AF:
Gnomad4 NFE
AF:
Gnomad4 OTH
AF:
Alfa
AF:
Hom.:
Bravo
AF:
Asia WGS
AF:
AC:
332
AN:
3478
ClinVar
Not reported inComputational scores
Source:
Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
Splicing
Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at