8-55963732-T-C

Variant names:

• chr8-55963732-T-C
• rs907425
• NM_002350.4:c.791-2983T>C

Variant summary

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

The NM_002350.4(LYN):​c.791-2983T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.502 in 152,140 control chromosomes in the GnomAD database, including 20,435 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 0.50 (20435 hom., cov: 33)
• Consequence: LYN NM_002350.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.145

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=-0.89).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.663 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LYN	NM_002350.4	c.791-2983T>C		intron_variant	Intron 8 of 12	ENST00000519728.6	NP_002341.1
LYN	NM_001111097.3	c.728-2983T>C		intron_variant	Intron 8 of 12		NP_001104567.1
LYN	XM_011517529.4	c.524-2983T>C		intron_variant	Intron 7 of 11		XP_011515831.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LYN	ENST00000519728.6	c.791-2983T>C		intron_variant	Intron 8 of 12	1	NM_002350.4	ENSP00000428924.1
LYN	ENST00000520220.6	c.728-2983T>C		intron_variant	Intron 8 of 12	1		ENSP00000428424.1
LYN	ENST00000420292.1	n.199-2983T>C		intron_variant	Intron 1 of 3	3

Frequencies

GnomAD3 genomes AF: 0.502 AC: 76346 AN: 152022 Hom.: 20406 Cov.: 33

Gnomad AFR AF: 0.670

Gnomad AMI AF: 0.687

Gnomad AMR AF: 0.415

Gnomad ASJ AF: 0.492

Gnomad EAS AF: 0.267

Gnomad SAS AF: 0.297

Gnomad FIN AF: 0.359

Gnomad MID AF: 0.611

Gnomad NFE AF: 0.471

Gnomad OTH AF: 0.539

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

GnomAD4 genome AF: 0.502 AC: 76425 AN: 152140 Hom.: 20435 Cov.: 33 AF XY: 0.491 AC XY: 36507 AN XY: 74368

Gnomad4 AFR AF: 0.670

Gnomad4 AMR AF: 0.414

Gnomad4 ASJ AF: 0.492

Gnomad4 EAS AF: 0.267

Gnomad4 SAS AF: 0.297

Gnomad4 FIN AF: 0.359

Gnomad4 NFE AF: 0.471

Gnomad4 OTH AF: 0.539

Alfa AF: 0.494 Hom.: 2368

Bravo AF: 0.514

Asia WGS AF: 0.307 AC: 1072 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	2.8
DANN	Benign	0.76

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: rs907425; hg19: chr8-56876291;