rs10485086

Positions:

• chr6-6554688-T-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.361+9607A>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 0.0847 in 152,230 control chromosomes in the GnomAD database, including 1,073 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 0.085 (1073 hom., cov: 33)
• Consequence: LY86-AS1 NR_026970.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.71

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=-0.96).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.242 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LY86-AS1	NR_026970.1	n.361+9607A>G		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
LY86-AS1	ENST00000429345.5	n.279+9607A>G		intron_variant, non_coding_transcript_variant		2

Frequencies

GnomAD3 genomes AF: 0.0846 AC: 12874 AN: 152112 Hom.: 1075 Cov.: 33

Gnomad AFR AF: 0.196

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0804

Gnomad ASJ AF: 0.00691

Gnomad EAS AF: 0.254

Gnomad SAS AF: 0.0228

Gnomad FIN AF: 0.0686

Gnomad MID AF: 0.0380

Gnomad NFE AF: 0.0179

Gnomad OTH AF: 0.0637

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

GnomAD4 genome AF: 0.0847 AC: 12888 AN: 152230 Hom.: 1073 Cov.: 33 AF XY: 0.0884 AC XY: 6582 AN XY: 74446

Gnomad4 AFR AF: 0.196

Gnomad4 AMR AF: 0.0805

Gnomad4 ASJ AF: 0.00691

Gnomad4 EAS AF: 0.253

Gnomad4 SAS AF: 0.0232

Gnomad4 FIN AF: 0.0686

Gnomad4 NFE AF: 0.0179

Gnomad4 OTH AF: 0.0626

Alfa AF: 0.0515 Hom.: 122

Bravo AF: 0.0922

Asia WGS AF: 0.118 AC: 411 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	0.095
DANN	Benign	0.54

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10485086; hg19: chr6-6554921;