8-55980329-G-C

Variant names:

• chr8-55980329-G-C
• rs7828483
• NM_002350.4:c.1050+10536G>C

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_002350.4(LYN):​c.1050+10536G>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 152,030 control chromosomes in the GnomAD database, including 8,627 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 (8624 hom., cov: 32)
  • Exomes 𝑓: 0.24 (3 hom.)
• Consequence: LYN NM_002350.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.206
• Publications: 3 publications found

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]

RN7SL798P (HGNC:46814): (RNA, 7SL, cytoplasmic 798, pseudogene)

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_002350.4. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LYN	NM_002350.4	MANE Select	c.1050+10536G>C		intron	N/A	NP_002341.1	P07948-1
	LYN	NM_001111097.3		c.987+10536G>C		intron	N/A	NP_001104567.1	P07948-2

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LYN	ENST00000519728.6	TSL:1 MANE Select	c.1050+10536G>C		intron	N/A	ENSP00000428924.1	P07948-1
	LYN	ENST00000520220.6	TSL:1	c.987+10536G>C		intron	N/A	ENSP00000428424.1	P07948-2
	LYN	ENST00000862998.1		c.1077+10536G>C		intron	N/A	ENSP00000533057.1

Frequencies

GnomAD3 genomes AF: 0.308 AC: 46809 AN: 151822 Hom.: 8594 Cov.: 32

Gnomad AFR AF: 0.507

Gnomad AMI AF: 0.398

Gnomad AMR AF: 0.254

Gnomad ASJ AF: 0.343

Gnomad EAS AF: 0.0283

Gnomad SAS AF: 0.140

Gnomad FIN AF: 0.183

Gnomad MID AF: 0.321

Gnomad NFE AF: 0.250

Gnomad OTH AF: 0.317

GnomAD4 exome AF: 0.245 AC: 23 AN: 94 Hom.: 3 Cov.: 0 AF XY: 0.212 AC XY: 14 AN XY: 66

African (AFR) AF: 0.500 AC: 1 AN: 2

American (AMR) AF: 0.500 AC: 2 AN: 4

Ashkenazi Jewish (ASJ) AC: 0 AN: 0

East Asian (EAS) AC: 0 AN: 0

South Asian (SAS) AF: 0.00 AC: 0 AN: 2

European-Finnish (FIN) AF: 0.500 AC: 5 AN: 10

Middle Eastern (MID) AC: 0 AN: 0

European-Non Finnish (NFE) AF: 0.189 AC: 14 AN: 74

Other (OTH) AF: 0.500 AC: 1 AN: 2

GnomAD4 genome AF: 0.309 AC: 46884 AN: 151936 Hom.: 8624 Cov.: 32 AF XY: 0.300 AC XY: 22277 AN XY: 74246

African (AFR) AF: 0.507 AC: 20988 AN: 41384

American (AMR) AF: 0.253 AC: 3864 AN: 15260

Ashkenazi Jewish (ASJ) AF: 0.343 AC: 1191 AN: 3468

East Asian (EAS) AF: 0.0284 AC: 147 AN: 5180

South Asian (SAS) AF: 0.140 AC: 674 AN: 4820

European-Finnish (FIN) AF: 0.183 AC: 1932 AN: 10544

Middle Eastern (MID) AF: 0.331 AC: 96 AN: 290

European-Non Finnish (NFE) AF: 0.250 AC: 16966 AN: 67966

Other (OTH) AF: 0.314 AC: 663 AN: 2112

Alfa AF: 0.124 Hom.: 200

Bravo AF: 0.323

Asia WGS AF: 0.119 AC: 416 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	0.92
DANN	Benign	0.55
PhyloP100		-0.21
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs7828483; hg19: chr8-56892888;