rs7774436

chr6-6361583-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.927+4772C>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 0.163 in 152,120 control chromosomes in the GnomAD database, including 2,299 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 0.16 (2299 hom., cov: 32)
  • Exomes 𝑓: 0.50 (0 hom.)
• Consequence: LY86-AS1 NR_026970.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.380

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=-0.91).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.246 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LY86-AS1	NR_026970.1	n.927+4772C>T		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
LY86-AS1	ENST00000429345.5	n.845+4772C>T		intron_variant, non_coding_transcript_variant		2

Frequencies

GnomAD3 genomes AF: 0.163 AC: 24752 AN: 152000 Hom.: 2297 Cov.: 32

Gnomad AFR AF: 0.250

Gnomad AMI AF: 0.0548

Gnomad AMR AF: 0.103

Gnomad ASJ AF: 0.140

Gnomad EAS AF: 0.00154

Gnomad SAS AF: 0.126

Gnomad FIN AF: 0.141

Gnomad MID AF: 0.241

Gnomad NFE AF: 0.144

Gnomad OTH AF: 0.153

GnomAD4 exome AF: 0.500 AC: 1 AN: 2 Hom.: 0 Cov.: 0 AC XY: 0 AN XY: 0

Gnomad4 NFE exome AF: 0.500

GnomAD4 genome AF: 0.163 AC: 24769 AN: 152118 Hom.: 2299 Cov.: 32 AF XY: 0.159 AC XY: 11834 AN XY: 74354

Gnomad4 AFR AF: 0.250

Gnomad4 AMR AF: 0.103

Gnomad4 ASJ AF: 0.140

Gnomad4 EAS AF: 0.00154

Gnomad4 SAS AF: 0.125

Gnomad4 FIN AF: 0.141

Gnomad4 NFE AF: 0.144

Gnomad4 OTH AF: 0.151

Alfa AF: 0.148 Hom.: 2492

Bravo AF: 0.164

Asia WGS AF: 0.0780 AC: 269 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
Cadd	Benign	1.0
Dann	Benign	0.40

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7774436; hg19: chr6-6361816;