chr6-6588648-A-C

Position:

• chr6-6588648-A-C

Variant summary

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

The NR_026970.1(LY86-AS1):​n.196-19159T>G variant causes a intron, non coding transcript change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.727 in 1,483,312 control chromosomes in the GnomAD database, including 392,704 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 0.71 (38176 hom., cov: 33)
  • Exomes 𝑓: 0.73 (354528 hom.)
• Consequence: LY86-AS1 NR_026970.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0680

Genes affected

LY86-AS1 (HGNC:26593): (LY86 antisense RNA 1)

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]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.729 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LY86-AS1	NR_026970.1	n.196-19159T>G		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
LY86-AS1	ENST00000429345.5	n.114-19159T>G		intron_variant, non_coding_transcript_variant		2

Frequencies

GnomAD3 genomes AF: 0.708 AC: 107659 AN: 152062 Hom.: 38163 Cov.: 33

Gnomad AFR AF: 0.651

Gnomad AMI AF: 0.589

Gnomad AMR AF: 0.713

Gnomad ASJ AF: 0.768

Gnomad EAS AF: 0.660

Gnomad SAS AF: 0.739

Gnomad FIN AF: 0.751

Gnomad MID AF: 0.728

Gnomad NFE AF: 0.735

Gnomad OTH AF: 0.703

GnomAD4 exome AF: 0.729 AC: 970839 AN: 1331132 Hom.: 354528 Cov.: 18 AF XY: 0.731 AC XY: 481575 AN XY: 658402

Gnomad4 AFR exome AF: 0.652

Gnomad4 AMR exome AF: 0.731

Gnomad4 ASJ exome AF: 0.775

Gnomad4 EAS exome AF: 0.672

Gnomad4 SAS exome AF: 0.749

Gnomad4 FIN exome AF: 0.741

Gnomad4 NFE exome AF: 0.730

Gnomad4 OTH exome AF: 0.732

GnomAD4 genome AF: 0.708 AC: 107706 AN: 152180 Hom.: 38176 Cov.: 33 AF XY: 0.707 AC XY: 52576 AN XY: 74408

Gnomad4 AFR AF: 0.651

Gnomad4 AMR AF: 0.713

Gnomad4 ASJ AF: 0.768

Gnomad4 EAS AF: 0.660

Gnomad4 SAS AF: 0.739

Gnomad4 FIN AF: 0.751

Gnomad4 NFE AF: 0.735

Gnomad4 OTH AF: 0.697

Alfa AF: 0.732 Hom.: 82706

Bravo AF: 0.704

Asia WGS AF: 0.655 AC: 2278 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	5.5
DANN	Benign	0.74

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: rs977785; hg19: chr6-6588881; COSMIC: COSV57913580; COSMIC: COSV57913580;