chr6-6554688-T-C

Variant names:

• chr6-6554688-T-C
• rs10485086
• ENST00000429345.5:n.279+9607A>G

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+9607A>G variant causes a intron 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 ENST00000429345.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.71
• Publications: 1 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=-0.96).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.242 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

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LY86-AS1	NR_026970.1		n.361+9607A>G		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LY86-AS1	ENST00000429345.5	TSL:2	n.279+9607A>G		intron	N/A
	LY86-AS1	ENST00000435641.5	TSL:2	n.482+9607A>G		intron	N/A
	LY86-AS1	ENST00000447858.1	TSL:3	n.149+32357A>G		intron	N/A

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

African (AFR) AF: 0.196 AC: 8122 AN: 41508

American (AMR) AF: 0.0805 AC: 1232 AN: 15300

Ashkenazi Jewish (ASJ) AF: 0.00691 AC: 24 AN: 3472

East Asian (EAS) AF: 0.253 AC: 1309 AN: 5174

South Asian (SAS) AF: 0.0232 AC: 112 AN: 4830

European-Finnish (FIN) AF: 0.0686 AC: 727 AN: 10604

Middle Eastern (MID) AF: 0.0408 AC: 12 AN: 294

European-Non Finnish (NFE) AF: 0.0179 AC: 1218 AN: 68026

Other (OTH) AF: 0.0626 AC: 132 AN: 2110

Alfa AF: 0.0353 Hom.: 456

Bravo AF: 0.0922

Asia WGS AF: 0.118 AC: 411 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	0.095
DANN	Benign	0.54
PhyloP100		-1.7

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs10485086;

hg19: chr6-6554921;