6-6569874-C-T

Variant names:

• chr6-6569874-C-T
• rs1999261
• ENST00000429345.5:n.114-385G>A

Variant summary

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

The ENST00000429345.5(LY86-AS1):​n.114-385G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.421 in 151,948 control chromosomes in the GnomAD database, including 13,374 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 0.42 (13374 hom., cov: 32)
• Consequence: LY86-AS1 ENST00000429345.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.659
• Publications: 4 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=-0.82).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.513 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

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LY86-AS1	NR_026970.1		n.196-385G>A		intron	N/A

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LY86-AS1	ENST00000429345.5	TSL:2	n.114-385G>A		intron	N/A
	LY86-AS1	ENST00000435641.5	TSL:2	n.389-5486G>A		intron	N/A
	LY86-AS1	ENST00000447858.1	TSL:3	n.149+17171G>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.421 AC: 63952 AN: 151830 Hom.: 13370 Cov.: 32

Gnomad AFR AF: 0.448

Gnomad AMI AF: 0.281

Gnomad AMR AF: 0.419

Gnomad ASJ AF: 0.411

Gnomad EAS AF: 0.530

Gnomad SAS AF: 0.438

Gnomad FIN AF: 0.469

Gnomad MID AF: 0.361

Gnomad NFE AF: 0.393

Gnomad OTH AF: 0.386

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

GnomAD4 genome AF: 0.421 AC: 63989 AN: 151948 Hom.: 13374 Cov.: 32 AF XY: 0.424 AC XY: 31477 AN XY: 74262

African (AFR) AF: 0.447 AC: 18539 AN: 41438

American (AMR) AF: 0.419 AC: 6394 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.411 AC: 1424 AN: 3468

East Asian (EAS) AF: 0.529 AC: 2736 AN: 5168

South Asian (SAS) AF: 0.437 AC: 2107 AN: 4818

European-Finnish (FIN) AF: 0.469 AC: 4941 AN: 10532

Middle Eastern (MID) AF: 0.364 AC: 107 AN: 294

European-Non Finnish (NFE) AF: 0.393 AC: 26677 AN: 67948

Other (OTH) AF: 0.384 AC: 809 AN: 2106

Alfa AF: 0.379 Hom.: 6464

Bravo AF: 0.424

Asia WGS AF: 0.436 AC: 1516 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	7.4
DANN	Benign	0.49
PhyloP100		0.66

Splicing

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

Other links and lift over

dbSNP: rs1999261; hg19: chr6-6570107;