chr6-6435212-T-C

Variant names:

• chr6-6435212-T-C
• rs6933874
• ENST00000429345.5:n.436+3364A>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.436+3364A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0573 in 152,144 control chromosomes in the GnomAD database, including 453 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 0.057 (453 hom., cov: 32)
• Consequence: LY86-AS1 ENST00000429345.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.942
• 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=-0.93).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.137 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.518+3364A>G		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LY86-AS1	ENST00000429345.5	TSL:2	n.436+3364A>G		intron	N/A
	LY86-AS1	ENST00000435641.5	TSL:2	n.639+3364A>G		intron	N/A
	LY86-AS1	ENST00000447858.1	TSL:3	n.306+3364A>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.0573 AC: 8710 AN: 152026 Hom.: 452 Cov.: 32

Gnomad AFR AF: 0.140

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0352

Gnomad ASJ AF: 0.0118

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.0207

Gnomad FIN AF: 0.0195

Gnomad MID AF: 0.0538

Gnomad NFE AF: 0.0281

Gnomad OTH AF: 0.0430

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

GnomAD4 genome AF: 0.0573 AC: 8723 AN: 152144 Hom.: 453 Cov.: 32 AF XY: 0.0550 AC XY: 4094 AN XY: 74404

African (AFR) AF: 0.140 AC: 5819 AN: 41508

American (AMR) AF: 0.0352 AC: 537 AN: 15264

Ashkenazi Jewish (ASJ) AF: 0.0118 AC: 41 AN: 3470

East Asian (EAS) AF: 0.00 AC: 0 AN: 5156

South Asian (SAS) AF: 0.0207 AC: 100 AN: 4832

European-Finnish (FIN) AF: 0.0195 AC: 207 AN: 10612

Middle Eastern (MID) AF: 0.0578 AC: 17 AN: 294

European-Non Finnish (NFE) AF: 0.0281 AC: 1912 AN: 67984

Other (OTH) AF: 0.0426 AC: 90 AN: 2114

Alfa AF: 0.0508 Hom.: 46

Bravo AF: 0.0618

Asia WGS AF: 0.0170 AC: 59 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	1.4
DANN	Benign	0.36
PhyloP100		-0.94
Mutation Taster		=100/0	polymorphism (auto)

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: rs6933874;

hg19: chr6-6435445;