rs554653

Variant names:

• chr6-6547254-C-A
• rs554653
• ENST00000429345.5:n.279+17041G>T

Variant summary

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

The ENST00000429345.5(LY86-AS1):​n.279+17041G>T variant causes a intron 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 ENST00000429345.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.43
• Publications: 5 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 (NFE) allele frequency at 95% confidence interval = 0.456 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.361+17041G>T		intron	N/A

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LY86-AS1	ENST00000429345.5	TSL:2	n.279+17041G>T		intron	N/A
	LY86-AS1	ENST00000435641.5	TSL:2	n.482+17041G>T		intron	N/A
	LY86-AS1	ENST00000447858.1	TSL:3	n.149+39791G>T		intron	N/A

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

African (AFR) AF: 0.335 AC: 13865 AN: 41354

American (AMR) AF: 0.392 AC: 5984 AN: 15250

Ashkenazi Jewish (ASJ) AF: 0.611 AC: 2118 AN: 3466

East Asian (EAS) AF: 0.132 AC: 683 AN: 5156

South Asian (SAS) AF: 0.427 AC: 2054 AN: 4808

European-Finnish (FIN) AF: 0.385 AC: 4050 AN: 10528

Middle Eastern (MID) AF: 0.599 AC: 176 AN: 294

European-Non Finnish (NFE) AF: 0.461 AC: 31281 AN: 67926

Other (OTH) AF: 0.435 AC: 916 AN: 2106

Alfa AF: 0.455 Hom.: 27014

Bravo AF: 0.400

Asia WGS AF: 0.296 AC: 1029 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	0.029
DANN	Benign	0.56
PhyloP100		-2.4

Splicing

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

Other links and lift over

dbSNP: rs554653; hg19: chr6-6547487;