chr6-6477616-G-A

Variant names:

• chr6-6477616-G-A
• rs9405302
• ENST00000429345.5:n.280-38884C>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.280-38884C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.323 in 152,028 control chromosomes in the GnomAD database, including 9,693 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 0.32 (9693 hom., cov: 32)
• Consequence: LY86-AS1 ENST00000429345.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.686
• Publications: 4 publications found

Genes affected

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

ENSG00000285717 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.81).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.568 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.362-38884C>T		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LY86-AS1	ENST00000429345.5	TSL:2	n.280-38884C>T		intron	N/A
	LY86-AS1	ENST00000435641.5	TSL:2	n.483-38884C>T		intron	N/A
	LY86-AS1	ENST00000447858.1	TSL:3	n.150-38884C>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.323 AC: 49034 AN: 151910 Hom.: 9685 Cov.: 32

Gnomad AFR AF: 0.529

Gnomad AMI AF: 0.145

Gnomad AMR AF: 0.293

Gnomad ASJ AF: 0.243

Gnomad EAS AF: 0.585

Gnomad SAS AF: 0.352

Gnomad FIN AF: 0.245

Gnomad MID AF: 0.348

Gnomad NFE AF: 0.201

Gnomad OTH AF: 0.298

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

GnomAD4 genome AF: 0.323 AC: 49082 AN: 152028 Hom.: 9693 Cov.: 32 AF XY: 0.326 AC XY: 24229 AN XY: 74322

African (AFR) AF: 0.529 AC: 21935 AN: 41458

American (AMR) AF: 0.292 AC: 4466 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.243 AC: 843 AN: 3470

East Asian (EAS) AF: 0.585 AC: 3016 AN: 5154

South Asian (SAS) AF: 0.352 AC: 1697 AN: 4818

European-Finnish (FIN) AF: 0.245 AC: 2597 AN: 10580

Middle Eastern (MID) AF: 0.340 AC: 100 AN: 294

European-Non Finnish (NFE) AF: 0.201 AC: 13667 AN: 67964

Other (OTH) AF: 0.299 AC: 629 AN: 2106

Alfa AF: 0.241 Hom.: 6752

Bravo AF: 0.337

Asia WGS AF: 0.445 AC: 1550 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
CADD	Benign	7.0
DANN	Benign	0.78
PhyloP100		0.69

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: rs9405302;

hg19: chr6-6477849;