rs554653

chr6-6547254-C-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.361+17041G>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 0.405 in 151,798 control chromosomes in the GnomAD database, including 12,994 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 0.41 (12994 hom., cov: 31)
• Consequence: LY86-AS1 NR_026970.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.43

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=-0.82).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.456 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LY86-AS1	NR_026970.1	n.361+17041G>T		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
LY86-AS1	ENST00000429345.5	n.279+17041G>T		intron_variant, non_coding_transcript_variant		2

Frequencies

GnomAD3 genomes AF: 0.405 AC: 61500 AN: 151682 Hom.: 12989 Cov.: 31

Gnomad AFR AF: 0.335

Gnomad AMI AF: 0.440

Gnomad AMR AF: 0.392

Gnomad ASJ AF: 0.611

Gnomad EAS AF: 0.133

Gnomad SAS AF: 0.426

Gnomad FIN AF: 0.385

Gnomad MID AF: 0.598

Gnomad NFE AF: 0.461

Gnomad OTH AF: 0.440

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

GnomAD4 genome AF: 0.405 AC: 61527 AN: 151798 Hom.: 12994 Cov.: 31 AF XY: 0.399 AC XY: 29608 AN XY: 74150

Gnomad4 AFR AF: 0.335

Gnomad4 AMR AF: 0.392

Gnomad4 ASJ AF: 0.611

Gnomad4 EAS AF: 0.132

Gnomad4 SAS AF: 0.427

Gnomad4 FIN AF: 0.385

Gnomad4 NFE AF: 0.461

Gnomad4 OTH AF: 0.435

Alfa AF: 0.460 Hom.: 21765

Bravo AF: 0.400

Asia WGS AF: 0.296 AC: 1029 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
Cadd	Benign	0.029
Dann	Benign	0.56

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs554653; hg19: chr6-6547487;