6-6592751-A-G

Position:

• chr6-6592751-A-G

Variant summary

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

The ENST00000230568.5(LY86):​c.136+3881A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.72 in 152,098 control chromosomes in the GnomAD database, including 39,394 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 0.72 (39394 hom., cov: 31)
• Consequence: LY86 ENST00000230568.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.600

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=-0.91).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.824 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LY86	NM_004271.4	c.136+3881A>G		intron_variant		ENST00000230568.5	NP_004262.1
LY86-AS1	NR_026970.1	n.196-23262T>C		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
LY86	ENST00000230568.5	c.136+3881A>G		intron_variant		1	NM_004271.4	ENSP00000230568	P1
LY86-AS1	ENST00000429345.5	n.114-23262T>C		intron_variant, non_coding_transcript_variant		2

Frequencies

GnomAD3 genomes AF: 0.720 AC: 109396 AN: 151980 Hom.: 39371 Cov.: 31

Gnomad AFR AF: 0.689

Gnomad AMI AF: 0.746

Gnomad AMR AF: 0.751

Gnomad ASJ AF: 0.810

Gnomad EAS AF: 0.845

Gnomad SAS AF: 0.696

Gnomad FIN AF: 0.685

Gnomad MID AF: 0.715

Gnomad NFE AF: 0.724

Gnomad OTH AF: 0.727

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

GnomAD4 genome AF: 0.720 AC: 109465 AN: 152098 Hom.: 39394 Cov.: 31 AF XY: 0.719 AC XY: 53463 AN XY: 74362

Gnomad4 AFR AF: 0.689

Gnomad4 AMR AF: 0.751

Gnomad4 ASJ AF: 0.810

Gnomad4 EAS AF: 0.844

Gnomad4 SAS AF: 0.697

Gnomad4 FIN AF: 0.685

Gnomad4 NFE AF: 0.724

Gnomad4 OTH AF: 0.723

Alfa AF: 0.725 Hom.: 6073

Bravo AF: 0.728

Asia WGS AF: 0.734 AC: 2554 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	1.4
DANN	Benign	0.56

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: rs1073897; hg19: chr6-6592984;