6-6591790-T-C

Variant names:

• chr6-6591790-T-C
• rs9328375
• NM_004271.4:c.136+2920T>C

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+2920T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.639 in 152,060 control chromosomes in the GnomAD database, including 31,209 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 0.64 (31209 hom., cov: 32)
• Consequence: LY86 NM_004271.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.983
• 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=-0.87).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.672 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LY86	NM_004271.4	c.136+2920T>C		intron_variant	Intron 1 of 4	ENST00000230568.5	NP_004262.1
LY86-AS1	NR_026970.1	n.196-22301A>G		intron_variant	Intron 1 of 7

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LY86	ENST00000230568.5	c.136+2920T>C		intron_variant	Intron 1 of 4	1	NM_004271.4	ENSP00000230568.3

Frequencies

GnomAD3 genomes AF: 0.639 AC: 97143 AN: 151942 Hom.: 31199 Cov.: 32

Gnomad AFR AF: 0.551

Gnomad AMI AF: 0.678

Gnomad AMR AF: 0.683

Gnomad ASJ AF: 0.745

Gnomad EAS AF: 0.645

Gnomad SAS AF: 0.663

Gnomad FIN AF: 0.648

Gnomad MID AF: 0.693

Gnomad NFE AF: 0.673

Gnomad OTH AF: 0.657

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

GnomAD4 genome AF: 0.639 AC: 97174 AN: 152060 Hom.: 31209 Cov.: 32 AF XY: 0.639 AC XY: 47511 AN XY: 74318

African (AFR) AF: 0.551 AC: 22826 AN: 41458

American (AMR) AF: 0.683 AC: 10435 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.745 AC: 2586 AN: 3472

East Asian (EAS) AF: 0.645 AC: 3336 AN: 5172

South Asian (SAS) AF: 0.662 AC: 3186 AN: 4814

European-Finnish (FIN) AF: 0.648 AC: 6839 AN: 10550

Middle Eastern (MID) AF: 0.697 AC: 205 AN: 294

European-Non Finnish (NFE) AF: 0.673 AC: 45768 AN: 67992

Other (OTH) AF: 0.651 AC: 1375 AN: 2112

Alfa AF: 0.672 Hom.: 56062

Bravo AF: 0.641

Asia WGS AF: 0.607 AC: 2114 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	5.6
DANN	Benign	0.65
PhyloP100		0.98
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: rs9328375; hg19: chr6-6592023;