rs1027986

Variant names:

• chr8-55969912-A-G
• rs1027986
• NM_002350.4:c.1050+119A>G

Your query was ambiguous. Multiple possible variants found:

• chr8-55969912-A-G
• chr8-55969912-A-T

Variant summary

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

The NM_002350.4(LYN):​c.1050+119A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.417 in 854,800 control chromosomes in the GnomAD database, including 77,681 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 0.43 (14606 hom., cov: 33)
  • Exomes 𝑓: 0.41 (63075 hom.)
• Consequence: LYN NM_002350.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0900

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=-0.79).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.452 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LYN	NM_002350.4	c.1050+119A>G		intron_variant	Intron 10 of 12	ENST00000519728.6	NP_002341.1
LYN	NM_001111097.3	c.987+119A>G		intron_variant	Intron 10 of 12		NP_001104567.1
LYN	XM_011517529.4	c.783+119A>G		intron_variant	Intron 9 of 11		XP_011515831.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LYN	ENST00000519728.6	c.1050+119A>G		intron_variant	Intron 10 of 12	1	NM_002350.4	ENSP00000428924.1
LYN	ENST00000520220.6	c.987+119A>G		intron_variant	Intron 10 of 12	1		ENSP00000428424.1
LYN	ENST00000420292.1	n.458+119A>G		intron_variant	Intron 3 of 3	3

Frequencies

GnomAD3 genomes AF: 0.432 AC: 65618 AN: 152024 Hom.: 14602 Cov.: 33

Gnomad AFR AF: 0.457

Gnomad AMI AF: 0.685

Gnomad AMR AF: 0.383

Gnomad ASJ AF: 0.485

Gnomad EAS AF: 0.248

Gnomad SAS AF: 0.289

Gnomad FIN AF: 0.345

Gnomad MID AF: 0.547

Gnomad NFE AF: 0.456

Gnomad OTH AF: 0.483

GnomAD4 exome AF: 0.414 AC: 290765 AN: 702658 Hom.: 63075 AF XY: 0.412 AC XY: 153712 AN XY: 372846

Gnomad4 AFR exome AF: 0.453

Gnomad4 AMR exome AF: 0.286

Gnomad4 ASJ exome AF: 0.514

Gnomad4 EAS exome AF: 0.261

Gnomad4 SAS exome AF: 0.303

Gnomad4 FIN exome AF: 0.355

Gnomad4 NFE exome AF: 0.451

Gnomad4 OTH exome AF: 0.436

GnomAD4 genome AF: 0.432 AC: 65658 AN: 152142 Hom.: 14606 Cov.: 33 AF XY: 0.422 AC XY: 31370 AN XY: 74372

Gnomad4 AFR AF: 0.457

Gnomad4 AMR AF: 0.383

Gnomad4 ASJ AF: 0.485

Gnomad4 EAS AF: 0.247

Gnomad4 SAS AF: 0.289

Gnomad4 FIN AF: 0.345

Gnomad4 NFE AF: 0.456

Gnomad4 OTH AF: 0.484

Alfa AF: 0.455 Hom.: 15610

Bravo AF: 0.437

Asia WGS AF: 0.283 AC: 987 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.79
CADD	Benign	6.1
DANN	Benign	0.55

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: rs1027986; hg19: chr8-56882471; COSMIC: COSV70205460;