rs2667985

Variant names:

• chr8-55967799-C-G
• rs2667985
• NM_002350.4:c.973+902C>G

Your query was ambiguous. Multiple possible variants found:

• chr8-55967799-C-G
• chr8-55967799-C-T

Variant summary

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

The ENST00000519728.6(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 ENST00000519728.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.117
• Publications: 5 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]

LYN Gene-Disease associations (from GenCC):

• autoinflammatory disease, systemic, with vasculitis

  Inheritance: AD Classification: STRONG, MODERATE Submitted by: Labcorp Genetics (formerly Invitae), Ambry Genetics

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000519728.6. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LYN	NM_002350.4	MANE Select	c.973+902C>G		intron	N/A	NP_002341.1
	LYN	NM_001111097.3		c.910+902C>G		intron	N/A	NP_001104567.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LYN	ENST00000519728.6	TSL:1 MANE Select	c.973+902C>G		intron	N/A	ENSP00000428924.1
	LYN	ENST00000520220.6	TSL:1	c.910+902C>G		intron	N/A	ENSP00000428424.1
	LYN	ENST00000420292.1	TSL:3	n.381+902C>G		intron	N/A

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

African (AFR) AF: 0.975 AC: 40520 AN: 41568

American (AMR) AF: 0.882 AC: 13503 AN: 15304

Ashkenazi Jewish (ASJ) AF: 0.909 AC: 3156 AN: 3472

East Asian (EAS) AF: 0.974 AC: 5054 AN: 5190

South Asian (SAS) AF: 0.845 AC: 4077 AN: 4824

European-Finnish (FIN) AF: 0.789 AC: 8327 AN: 10560

Middle Eastern (MID) AF: 0.935 AC: 275 AN: 294

European-Non Finnish (NFE) AF: 0.866 AC: 58932 AN: 68012

Other (OTH) AF: 0.908 AC: 1919 AN: 2114

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 v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	2.0
DANN	Benign	0.28
PhyloP100		0.12
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs2667985; hg19: chr8-56880358;