rs10095917

Positions:

• chr8-55917701-C-T

Variant summary

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

The NM_002350.4(LYN):​c.-5-24154C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.25 in 152,108 control chromosomes in the GnomAD database, including 5,318 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 0.25 (5318 hom., cov: 32)
• Consequence: LYN NM_002350.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0500

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 = 0.361 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LYN	NM_002350.4	c.-5-24154C>T		intron_variant		ENST00000519728.6
LYN	NM_001111097.3	c.-5-24154C>T		intron_variant
LYN	XM_011517529.4	c.-135-28747C>T		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
LYN	ENST00000519728.6	c.-5-24154C>T		intron_variant		1	NM_002350.4	P4
LYN	ENST00000520220.6	c.-5-24154C>T		intron_variant		1		A1

Frequencies

GnomAD3 genomes AF: 0.250 AC: 37934 AN: 151990 Hom.: 5305 Cov.: 32

Gnomad AFR AF: 0.365

Gnomad AMI AF: 0.367

Gnomad AMR AF: 0.216

Gnomad ASJ AF: 0.290

Gnomad EAS AF: 0.0245

Gnomad SAS AF: 0.158

Gnomad FIN AF: 0.149

Gnomad MID AF: 0.377

Gnomad NFE AF: 0.221

Gnomad OTH AF: 0.265

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

GnomAD4 genome AF: 0.250 AC: 37983 AN: 152108 Hom.: 5318 Cov.: 32 AF XY: 0.244 AC XY: 18133 AN XY: 74364

Gnomad4 AFR AF: 0.366

Gnomad4 AMR AF: 0.216

Gnomad4 ASJ AF: 0.290

Gnomad4 EAS AF: 0.0246

Gnomad4 SAS AF: 0.159

Gnomad4 FIN AF: 0.149

Gnomad4 NFE AF: 0.221

Gnomad4 OTH AF: 0.262

Alfa AF: 0.231 Hom.: 2428

Bravo AF: 0.260

Asia WGS AF: 0.114 AC: 397 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	1.1
DANN	Benign	0.14

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: rs10095917; hg19: chr8-56830260;