6-6610376-C-T

Variant names:

• chr6-6610376-C-T
• rs7740529
• NM_004271.4:c.137-14550C>T

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 6 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=-0.92).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.546 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.137-14550C>T		intron	N/A	NP_004262.1
	LY86-AS1	NR_026970.1		n.195+12256G>A		intron	N/A

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LY86	ENST00000230568.5	TSL:1 MANE Select	c.137-14550C>T		intron	N/A	ENSP00000230568.3
	LY86	ENST00000379953.6	TSL:5	c.137-14550C>T		intron	N/A	ENSP00000369286.1
	LY86-AS1	ENST00000429345.5	TSL:2	n.113+12256G>A		intron	N/A

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

African (AFR) AF: 0.552 AC: 22895 AN: 41448

American (AMR) AF: 0.193 AC: 2950 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.141 AC: 488 AN: 3470

East Asian (EAS) AF: 0.296 AC: 1528 AN: 5164

South Asian (SAS) AF: 0.210 AC: 1013 AN: 4816

European-Finnish (FIN) AF: 0.186 AC: 1975 AN: 10594

Middle Eastern (MID) AF: 0.163 AC: 48 AN: 294

European-Non Finnish (NFE) AF: 0.106 AC: 7186 AN: 68004

Other (OTH) AF: 0.209 AC: 441 AN: 2112

Alfa AF: 0.148 Hom.: 3469

Bravo AF: 0.265

Asia WGS AF: 0.309 AC: 1073 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.83
DANN	Benign	0.30
PhyloP100		-0.82
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: rs7740529; hg19: chr6-6610609;