rs9405302

chr6-6477616-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.362-38884C>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 0.323 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 NR_026970.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.686

Genes affected

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

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LY86-AS1	NR_026970.1	n.362-38884C>T		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
LY86-AS1	ENST00000429345.5	n.280-38884C>T		intron_variant, non_coding_transcript_variant		2
	ENST00000649026.1	n.203-11260G>A		intron_variant, non_coding_transcript_variant

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

Gnomad4 AFR AF: 0.529

Gnomad4 AMR AF: 0.292

Gnomad4 ASJ AF: 0.243

Gnomad4 EAS AF: 0.585

Gnomad4 SAS AF: 0.352

Gnomad4 FIN AF: 0.245

Gnomad4 NFE AF: 0.201

Gnomad4 OTH AF: 0.299

Alfa AF: 0.228 Hom.: 4468

Bravo AF: 0.337

Asia WGS AF: 0.445 AC: 1550 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
Cadd	Benign	7.0
Dann	Benign	0.78

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs9405302; hg19: chr6-6477849;