8-55980329-G-C

Variant names:

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

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

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 rank	MANE	Protein	UniProt
LYN	NM_002350.4	c.1050+10536G>C		intron_variant	Intron 10 of 12	ENST00000519728.6	NP_002341.1
LYN	NM_001111097.3	c.987+10536G>C		intron_variant	Intron 10 of 12		NP_001104567.1
LYN	XM_011517529.4	c.783+10536G>C		intron_variant	Intron 9 of 11		XP_011515831.2
RN7SL798P		n.55980329G>C		intragenic_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LYN	ENST00000519728.6	c.1050+10536G>C		intron_variant	Intron 10 of 12	1	NM_002350.4	ENSP00000428924.1
LYN	ENST00000520220.6	c.987+10536G>C		intron_variant	Intron 10 of 12	1		ENSP00000428424.1
RN7SL798P	ENST00000468562.3	n.212C>G		non_coding_transcript_exon_variant	Exon 1 of 1	6
LYN	ENST00000420292.1	n.458+10536G>C		intron_variant	Intron 3 of 3	3

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

Gnomad4 AFR exome AF: 0.500

Gnomad4 AMR exome AF: 0.500

Gnomad4 SAS exome AF: 0.00

Gnomad4 FIN exome AF: 0.500

Gnomad4 NFE exome AF: 0.189

Gnomad4 OTH exome AF: 0.500

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

Gnomad4 AFR AF: 0.507

Gnomad4 AMR AF: 0.253

Gnomad4 ASJ AF: 0.343

Gnomad4 EAS AF: 0.0284

Gnomad4 SAS AF: 0.140

Gnomad4 FIN AF: 0.183

Gnomad4 NFE AF: 0.250

Gnomad4 OTH AF: 0.314

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 v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	0.92
DANN	Benign	0.55

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: rs7828483; hg19: chr8-56892888;