rs1980042

chr8-55900083-A-G

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_002350.4(LYN):c.-6+19980A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.436 in 152,000 control chromosomes in the GnomAD database, including 15,109 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 0.44 (15109 hom., cov: 32)
• Consequence: LYN NM_002350.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.193

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]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.541 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LYN	NM_002350.4	c.-6+19980A>G		intron_variant		ENST00000519728.6
LYN	NM_001111097.3	c.-6+19980A>G		intron_variant
LYN	XM_011517529.4	c.-136+19980A>G		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
LYN	ENST00000519728.6	c.-6+19980A>G		intron_variant		1	NM_002350.4	P4
LYN	ENST00000520220.6	c.-6+19980A>G		intron_variant		1		A1

Frequencies

GnomAD3 genomes AF: 0.436 AC: 66194 AN: 151882 Hom.: 15077 Cov.: 32

Gnomad AFR AF: 0.547

Gnomad AMI AF: 0.568

Gnomad AMR AF: 0.378

Gnomad ASJ AF: 0.415

Gnomad EAS AF: 0.206

Gnomad SAS AF: 0.330

Gnomad FIN AF: 0.330

Gnomad MID AF: 0.535

Gnomad NFE AF: 0.422

Gnomad OTH AF: 0.433

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.436 AC: 66264 AN: 152000 Hom.: 15109 Cov.: 32 AF XY: 0.427 AC XY: 31747 AN XY: 74288

Gnomad4 AFR AF: 0.547

Gnomad4 AMR AF: 0.378

Gnomad4 ASJ AF: 0.415

Gnomad4 EAS AF: 0.207

Gnomad4 SAS AF: 0.328

Gnomad4 FIN AF: 0.330

Gnomad4 NFE AF: 0.422

Gnomad4 OTH AF: 0.428

Alfa AF: 0.424 Hom.: 1775

Bravo AF: 0.444

Asia WGS AF: 0.292 AC: 1018 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
Cadd	Benign	2.4
Dann	Benign	0.48

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

Other links and lift over

dbSNP: rs1980042; hg19: chr8-56812642;