rs2719253

chr8-55992607-T-C

Variant summary

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

The NM_002350.4(LYN):c.1051-5739T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.265 in 152,144 control chromosomes in the GnomAD database, including 5,793 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 0.26 (5793 hom., cov: 32)
• Consequence: LYN NM_002350.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.355

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=-0.9).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.349 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LYN	NM_002350.4	c.1051-5739T>C		intron_variant		ENST00000519728.6
LYN	NM_001111097.3	c.988-5739T>C		intron_variant
LYN	XM_011517529.4	c.784-5739T>C		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
LYN	ENST00000519728.6	c.1051-5739T>C		intron_variant		1	NM_002350.4	P4
LYN	ENST00000520220.6	c.988-5739T>C		intron_variant		1		A1
LYN	ENST00000420292.1	n.459-5739T>C		intron_variant, non_coding_transcript_variant		3

Frequencies

GnomAD3 genomes AF: 0.265 AC: 40246 AN: 152026 Hom.: 5787 Cov.: 32

Gnomad AFR AF: 0.354

Gnomad AMI AF: 0.396

Gnomad AMR AF: 0.242

Gnomad ASJ AF: 0.341

Gnomad EAS AF: 0.0268

Gnomad SAS AF: 0.142

Gnomad FIN AF: 0.183

Gnomad MID AF: 0.316

Gnomad NFE AF: 0.249

Gnomad OTH AF: 0.284

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

GnomAD4 genome AF: 0.265 AC: 40280 AN: 152144 Hom.: 5793 Cov.: 32 AF XY: 0.258 AC XY: 19168 AN XY: 74386

Gnomad4 AFR AF: 0.354

Gnomad4 AMR AF: 0.242

Gnomad4 ASJ AF: 0.341

Gnomad4 EAS AF: 0.0268

Gnomad4 SAS AF: 0.142

Gnomad4 FIN AF: 0.183

Gnomad4 NFE AF: 0.249

Gnomad4 OTH AF: 0.281

Alfa AF: 0.254 Hom.: 681

Bravo AF: 0.275

Asia WGS AF: 0.109 AC: 381 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
Cadd	Benign	7.1
Dann	Benign	0.69

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: rs2719253; hg19: chr8-56905166;