rs4959389

Variant names:

• chr6-6586602-G-A
• rs4959389
• ENST00000429345.5:n.114-17113C>T

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000429345.5(LY86-AS1):​n.114-17113C>T variant causes a intron 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 ENST00000429345.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.613
• Publications: 5 publications found

Genes affected

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 (EAS) allele frequency at 95% confidence interval = 0.909 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000429345.5. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LY86-AS1	NR_026970.1		n.196-17113C>T		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LY86-AS1	ENST00000429345.5	TSL:2	n.114-17113C>T		intron	N/A
	LY86-AS1	ENST00000435641.5	TSL:2	n.388+4554C>T		intron	N/A
	LY86-AS1	ENST00000447858.1	TSL:3	n.149+443C>T		intron	N/A

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

African (AFR) AF: 0.908 AC: 37726 AN: 41544

American (AMR) AF: 0.831 AC: 12714 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.856 AC: 2973 AN: 3472

East Asian (EAS) AF: 0.931 AC: 4826 AN: 5182

South Asian (SAS) AF: 0.888 AC: 4289 AN: 4828

European-Finnish (FIN) AF: 0.790 AC: 8379 AN: 10600

Middle Eastern (MID) AF: 0.905 AC: 266 AN: 294

European-Non Finnish (NFE) AF: 0.792 AC: 53856 AN: 67994

Other (OTH) AF: 0.820 AC: 1728 AN: 2108

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 v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	0.80
DANN	Benign	0.69
PhyloP100		-0.61

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs4959389;

hg19: chr6-6586835;