rs4959389

Positions:

• chr6-6586602-G-A

Variant summary

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

The NR_026970.1(LY86-AS1):​n.196-17113C>T 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 0.837 in 152,226 control chromosomes in the GnomAD database, including 53,561 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 0.84 (53561 hom., cov: 32)
• Consequence: LY86-AS1 NR_026970.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.613

Genes affected

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=-0.87).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.909 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LY86-AS1	NR_026970.1	n.196-17113C>T		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
LY86-AS1	ENST00000429345.5	n.114-17113C>T		intron_variant, non_coding_transcript_variant		2

Frequencies

GnomAD3 genomes AF: 0.837 AC: 127310 AN: 152108 Hom.: 53516 Cov.: 32

Gnomad AFR AF: 0.908

Gnomad AMI AF: 0.719

Gnomad AMR AF: 0.831

Gnomad ASJ AF: 0.856

Gnomad EAS AF: 0.931

Gnomad SAS AF: 0.888

Gnomad FIN AF: 0.790

Gnomad MID AF: 0.899

Gnomad NFE AF: 0.792

Gnomad OTH AF: 0.824

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

GnomAD4 genome AF: 0.837 AC: 127413 AN: 152226 Hom.: 53561 Cov.: 32 AF XY: 0.838 AC XY: 62401 AN XY: 74438

Gnomad4 AFR AF: 0.908

Gnomad4 AMR AF: 0.831

Gnomad4 ASJ AF: 0.856

Gnomad4 EAS AF: 0.931

Gnomad4 SAS AF: 0.888

Gnomad4 FIN AF: 0.790

Gnomad4 NFE AF: 0.792

Gnomad4 OTH AF: 0.820

Alfa AF: 0.808 Hom.: 10077

Bravo AF: 0.845

Asia WGS AF: 0.873 AC: 3038 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	0.80
DANN	Benign	0.69

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Other links and lift over

dbSNP: rs4959389; hg19: chr6-6586835;