rs16922463

Positions:

• chr8-55949110-C-A

Variant summary

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

The NM_002350.4(LYN):​c.285-1349C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.238 in 152,060 control chromosomes in the GnomAD database, including 5,239 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 0.24 (5239 hom., cov: 32)
• Consequence: LYN NM_002350.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.161

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=-0.91).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.399 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LYN	NM_002350.4	c.285-1349C>A		intron_variant		ENST00000519728.6	NP_002341.1
LYN	NM_001111097.3	c.222-1349C>A		intron_variant			NP_001104567.1
LYN	XM_011517529.4	c.18-1349C>A		intron_variant			XP_011515831.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
LYN	ENST00000519728.6	c.285-1349C>A		intron_variant		1	NM_002350.4	ENSP00000428924.1
LYN	ENST00000520220.6	c.222-1349C>A		intron_variant		1		ENSP00000428424.1
LYN	ENST00000520050.1	c.285-1349C>A		intron_variant		4		ENSP00000428313.1

Frequencies

GnomAD3 genomes AF: 0.238 AC: 36099 AN: 151942 Hom.: 5224 Cov.: 32

Gnomad AFR AF: 0.404

Gnomad AMI AF: 0.298

Gnomad AMR AF: 0.189

Gnomad ASJ AF: 0.230

Gnomad EAS AF: 0.0246

Gnomad SAS AF: 0.141

Gnomad FIN AF: 0.0998

Gnomad MID AF: 0.307

Gnomad NFE AF: 0.191

Gnomad OTH AF: 0.231

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

GnomAD4 genome AF: 0.238 AC: 36150 AN: 152060 Hom.: 5239 Cov.: 32 AF XY: 0.230 AC XY: 17111 AN XY: 74354

Gnomad4 AFR AF: 0.404

Gnomad4 AMR AF: 0.189

Gnomad4 ASJ AF: 0.230

Gnomad4 EAS AF: 0.0247

Gnomad4 SAS AF: 0.140

Gnomad4 FIN AF: 0.0998

Gnomad4 NFE AF: 0.191

Gnomad4 OTH AF: 0.228

Alfa AF: 0.201 Hom.: 2316

Bravo AF: 0.251

Asia WGS AF: 0.0970 AC: 337 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.16
DANN	Benign	0.43

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.010		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: rs16922463; hg19: chr8-56861669; COSMIC: COSV72923516;