rs16922508

chr8-55979671-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.1050+9878T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.309 in 152,036 control chromosomes in the GnomAD database, including 8,634 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 0.31 (8634 hom., cov: 31)
• Consequence: LYN NM_002350.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.00600

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=-0.93).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.501 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LYN	NM_002350.4	c.1050+9878T>C		intron_variant		ENST00000519728.6
LYN	NM_001111097.3	c.987+9878T>C		intron_variant
LYN	XM_011517529.4	c.783+9878T>C		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
LYN	ENST00000519728.6	c.1050+9878T>C		intron_variant		1	NM_002350.4	P4
LYN	ENST00000520220.6	c.987+9878T>C		intron_variant		1		A1
LYN	ENST00000420292.1	n.458+9878T>C		intron_variant, non_coding_transcript_variant		3

Frequencies

GnomAD3 genomes AF: 0.308 AC: 46856 AN: 151918 Hom.: 8605 Cov.: 31

Gnomad AFR AF: 0.506

Gnomad AMI AF: 0.405

Gnomad AMR AF: 0.254

Gnomad ASJ AF: 0.342

Gnomad EAS AF: 0.0285

Gnomad SAS AF: 0.140

Gnomad FIN AF: 0.183

Gnomad MID AF: 0.329

Gnomad NFE AF: 0.250

Gnomad OTH AF: 0.318

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

GnomAD4 genome AF: 0.309 AC: 46932 AN: 152036 Hom.: 8634 Cov.: 31 AF XY: 0.300 AC XY: 22300 AN XY: 74330

Gnomad4 AFR AF: 0.507

Gnomad4 AMR AF: 0.254

Gnomad4 ASJ AF: 0.342

Gnomad4 EAS AF: 0.0286

Gnomad4 SAS AF: 0.140

Gnomad4 FIN AF: 0.183

Gnomad4 NFE AF: 0.250

Gnomad4 OTH AF: 0.315

Alfa AF: 0.275 Hom.: 6151

Bravo AF: 0.324

Asia WGS AF: 0.120 AC: 419 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
Cadd	Benign	3.0
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: rs16922508; hg19: chr8-56892230;