rs7740529

chr6-6610376-C-T

Variant summary

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

The NM_004271.4(LY86):c.137-14550C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.254 in 152,096 control chromosomes in the GnomAD database, including 7,672 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 0.25 (7672 hom., cov: 33)
• Consequence: LY86 NM_004271.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.823

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=-0.92).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.546 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LY86	NM_004271.4	c.137-14550C>T		intron_variant		ENST00000230568.5
LY86-AS1	NR_026970.1	n.195+12256G>A		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
LY86	ENST00000230568.5	c.137-14550C>T		intron_variant		1	NM_004271.4	P1
LY86-AS1	ENST00000429345.5	n.113+12256G>A		intron_variant, non_coding_transcript_variant		2

Frequencies

GnomAD3 genomes AF: 0.253 AC: 38481 AN: 151978 Hom.: 7634 Cov.: 33

Gnomad AFR AF: 0.552

Gnomad AMI AF: 0.0640

Gnomad AMR AF: 0.193

Gnomad ASJ AF: 0.141

Gnomad EAS AF: 0.296

Gnomad SAS AF: 0.209

Gnomad FIN AF: 0.186

Gnomad MID AF: 0.158

Gnomad NFE AF: 0.106

Gnomad OTH AF: 0.204

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

GnomAD4 genome AF: 0.254 AC: 38582 AN: 152096 Hom.: 7672 Cov.: 33 AF XY: 0.257 AC XY: 19105 AN XY: 74344

Gnomad4 AFR AF: 0.552

Gnomad4 AMR AF: 0.193

Gnomad4 ASJ AF: 0.141

Gnomad4 EAS AF: 0.296

Gnomad4 SAS AF: 0.210

Gnomad4 FIN AF: 0.186

Gnomad4 NFE AF: 0.106

Gnomad4 OTH AF: 0.209

Alfa AF: 0.130 Hom.: 1908

Bravo AF: 0.265

Asia WGS AF: 0.309 AC: 1073 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
Cadd	Benign	0.83
Dann	Benign	0.30

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: rs7740529; hg19: chr6-6610609;