rs4061077

Positions:

• chr8-55990883-G-A
• chr8-55990883-G-T

Variant summary

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

The NM_002350.4(LYN):​c.1051-7463G>A 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 152,096 control chromosomes in the GnomAD database, including 5,794 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 (5794 hom., cov: 32)
• Consequence: LYN NM_002350.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.07

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=-0.92).
• 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	Protein	UniProt
LYN	NM_002350.4	c.1051-7463G>A		intron_variant		ENST00000519728.6	NP_002341.1
LYN	NM_001111097.3	c.988-7463G>A		intron_variant			NP_001104567.1
LYN	XM_011517529.4	c.784-7463G>A		intron_variant			XP_011515831.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
LYN	ENST00000519728.6	c.1051-7463G>A		intron_variant		1	NM_002350.4	ENSP00000428924	P4
LYN	ENST00000520220.6	c.988-7463G>A		intron_variant		1		ENSP00000428424	A1
LYN	ENST00000420292.1	n.459-7463G>A		intron_variant, non_coding_transcript_variant		3

Frequencies

GnomAD3 genomes AF: 0.265 AC: 40255 AN: 151978 Hom.: 5787 Cov.: 32

Gnomad AFR AF: 0.354

Gnomad AMI AF: 0.399

Gnomad AMR AF: 0.243

Gnomad ASJ AF: 0.342

Gnomad EAS AF: 0.0287

Gnomad SAS AF: 0.142

Gnomad FIN AF: 0.183

Gnomad MID AF: 0.316

Gnomad NFE AF: 0.249

Gnomad OTH AF: 0.285

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

GnomAD4 genome AF: 0.265 AC: 40289 AN: 152096 Hom.: 5794 Cov.: 32 AF XY: 0.258 AC XY: 19170 AN XY: 74384

Gnomad4 AFR AF: 0.354

Gnomad4 AMR AF: 0.242

Gnomad4 ASJ AF: 0.342

Gnomad4 EAS AF: 0.0288

Gnomad4 SAS AF: 0.142

Gnomad4 FIN AF: 0.183

Gnomad4 NFE AF: 0.249

Gnomad4 OTH AF: 0.282

Alfa AF: 0.137 Hom.: 250

Bravo AF: 0.275

Asia WGS AF: 0.113 AC: 395 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.058
DANN	Benign	0.17

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: rs4061077; hg19: chr8-56903442;