rs6983130

chr8-55880680-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+577A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.183 in 152,258 control chromosomes in the GnomAD database, including 2,621 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 0.18 (2621 hom., cov: 33)
• Consequence: LYN NM_002350.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.22

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=-0.8).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.223 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LYN	NM_002350.4	c.-6+577A>G		intron_variant		ENST00000519728.6
LYN	NM_001111097.3	c.-6+577A>G		intron_variant
LYN	XM_011517529.4	c.-136+577A>G		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
LYN	ENST00000519728.6	c.-6+577A>G		intron_variant		1	NM_002350.4	P4
LYN	ENST00000520220.6	c.-6+577A>G		intron_variant		1		A1

Frequencies

GnomAD3 genomes AF: 0.183 AC: 27908 AN: 152140 Hom.: 2614 Cov.: 33

Gnomad AFR AF: 0.172

Gnomad AMI AF: 0.488

Gnomad AMR AF: 0.158

Gnomad ASJ AF: 0.198

Gnomad EAS AF: 0.126

Gnomad SAS AF: 0.234

Gnomad FIN AF: 0.134

Gnomad MID AF: 0.244

Gnomad NFE AF: 0.199

Gnomad OTH AF: 0.186

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

GnomAD4 genome AF: 0.183 AC: 27934 AN: 152258 Hom.: 2621 Cov.: 33 AF XY: 0.180 AC XY: 13381 AN XY: 74458

Gnomad4 AFR AF: 0.173

Gnomad4 AMR AF: 0.158

Gnomad4 ASJ AF: 0.198

Gnomad4 EAS AF: 0.126

Gnomad4 SAS AF: 0.235

Gnomad4 FIN AF: 0.134

Gnomad4 NFE AF: 0.199

Gnomad4 OTH AF: 0.184

Alfa AF: 0.183 Hom.: 323

Bravo AF: 0.182

Asia WGS AF: 0.193 AC: 670 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.80
Cadd	Benign	0.47
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

Other links and lift over

dbSNP: rs6983130; hg19: chr8-56793239;