rs2667985

chr8-55967799-C-Gchr8-55967799-C-T

Variant summary

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

The NM_002350.4(LYN):c.973+902C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.897 in 152,250 control chromosomes in the GnomAD database, including 61,639 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 0.90 (61639 hom., cov: 31)
• Consequence: LYN NM_002350.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.117

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=-0.86).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.967 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LYN	NM_002350.4	c.973+902C>G		intron_variant		ENST00000519728.6
LYN	NM_001111097.3	c.910+902C>G		intron_variant
LYN	XM_011517529.4	c.706+902C>G		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
LYN	ENST00000519728.6	c.973+902C>G		intron_variant		1	NM_002350.4	P4
LYN	ENST00000520220.6	c.910+902C>G		intron_variant		1		A1
LYN	ENST00000420292.1	n.381+902C>G		intron_variant, non_coding_transcript_variant		3

Frequencies

GnomAD3 genomes AF: 0.897 AC: 136521 AN: 152132 Hom.: 61578 Cov.: 31

Gnomad AFR AF: 0.975

Gnomad AMI AF: 0.963

Gnomad AMR AF: 0.882

Gnomad ASJ AF: 0.909

Gnomad EAS AF: 0.974

Gnomad SAS AF: 0.845

Gnomad FIN AF: 0.789

Gnomad MID AF: 0.940

Gnomad NFE AF: 0.866

Gnomad OTH AF: 0.907

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

GnomAD4 genome AF: 0.897 AC: 136641 AN: 152250 Hom.: 61639 Cov.: 31 AF XY: 0.892 AC XY: 66363 AN XY: 74422

Gnomad4 AFR AF: 0.975

Gnomad4 AMR AF: 0.882

Gnomad4 ASJ AF: 0.909

Gnomad4 EAS AF: 0.974

Gnomad4 SAS AF: 0.845

Gnomad4 FIN AF: 0.789

Gnomad4 NFE AF: 0.866

Gnomad4 OTH AF: 0.908

Alfa AF: 0.877 Hom.: 7288

Bravo AF: 0.910

Asia WGS AF: 0.914 AC: 3178 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
Cadd	Benign	2.0
Dann	Benign	0.28

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: rs2667985; hg19: chr8-56880358;