6-6612234-G-C

Variant names:

• chr6-6612234-G-C
• rs2326810
• NM_004271.4:c.137-12692G>C

Variant summary

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

The NM_004271.4(LY86):​c.137-12692G>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0789 in 152,262 control chromosomes in the GnomAD database, including 561 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 0.079 (561 hom., cov: 33)
• Consequence: LY86 NM_004271.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.14

Genes affected

LY86 (HGNC:16837): (lymphocyte antigen 86) Acts upstream of or within positive regulation of lipopolysaccharide-mediated signaling pathway. Predicted to be located in extracellular space. [provided by Alliance of Genome Resources, Apr 2022]

LY86-AS1 (HGNC:26593): (LY86 antisense RNA 1)

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.03).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.162 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LY86	NM_004271.4	c.137-12692G>C		intron_variant	Intron 1 of 4	ENST00000230568.5	NP_004262.1
LY86-AS1	NR_026970.1	n.195+10398C>G		intron_variant	Intron 1 of 7

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LY86	ENST00000230568.5	c.137-12692G>C		intron_variant	Intron 1 of 4	1	NM_004271.4	ENSP00000230568.3

Frequencies

GnomAD3 genomes AF: 0.0788 AC: 11988 AN: 152144 Hom.: 554 Cov.: 33

Gnomad AFR AF: 0.0706

Gnomad AMI AF: 0.0340

Gnomad AMR AF: 0.121

Gnomad ASJ AF: 0.0778

Gnomad EAS AF: 0.172

Gnomad SAS AF: 0.0978

Gnomad FIN AF: 0.101

Gnomad MID AF: 0.0348

Gnomad NFE AF: 0.0634

Gnomad OTH AF: 0.0723

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

GnomAD4 genome AF: 0.0789 AC: 12009 AN: 152262 Hom.: 561 Cov.: 33 AF XY: 0.0820 AC XY: 6105 AN XY: 74454

Gnomad4 AFR AF: 0.0705

Gnomad4 AMR AF: 0.121

Gnomad4 ASJ AF: 0.0778

Gnomad4 EAS AF: 0.171

Gnomad4 SAS AF: 0.0981

Gnomad4 FIN AF: 0.101

Gnomad4 NFE AF: 0.0635

Gnomad4 OTH AF: 0.0777

Alfa AF: 0.0305 Hom.: 21

Bravo AF: 0.0810

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.47
DANN	Benign	0.29

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: rs2326810; hg19: chr6-6612467;