NM_004271.4:c.136+3881A>G

Variant names:

• chr6-6592751-A-G
• rs1073897
• NM_004271.4:c.136+3881A>G

Variant summary

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

The NM_004271.4(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 NM_004271.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.600
• Publications: 2 publications found

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

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_004271.4. 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
	LY86	NM_004271.4	MANE Select	c.136+3881A>G		intron	N/A	NP_004262.1
	LY86-AS1	NR_026970.1		n.196-23262T>C		intron	N/A

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LY86	ENST00000230568.5	TSL:1 MANE Select	c.136+3881A>G		intron	N/A	ENSP00000230568.3
	LY86	ENST00000379953.6	TSL:5	c.136+3881A>G		intron	N/A	ENSP00000369286.1
	LY86-AS1	ENST00000429345.5	TSL:2	n.114-23262T>C		intron	N/A

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

African (AFR) AF: 0.689 AC: 28609 AN: 41500

American (AMR) AF: 0.751 AC: 11473 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.810 AC: 2814 AN: 3472

East Asian (EAS) AF: 0.844 AC: 4381 AN: 5188

South Asian (SAS) AF: 0.697 AC: 3362 AN: 4826

European-Finnish (FIN) AF: 0.685 AC: 7228 AN: 10548

Middle Eastern (MID) AF: 0.721 AC: 212 AN: 294

European-Non Finnish (NFE) AF: 0.724 AC: 49179 AN: 67970

Other (OTH) AF: 0.723 AC: 1528 AN: 2114

Alfa AF: 0.725 Hom.: 6123

Bravo AF: 0.728

Asia WGS AF: 0.734 AC: 2554 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	1.4
DANN	Benign	0.56
PhyloP100		-0.60
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs1073897; hg19: chr6-6592984;