rs7774436

Variant names:

• chr6-6361583-G-A
• rs7774436
• ENST00000435641.5:n.1827C>T

Variant summary

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

The ENST00000435641.5(LY86-AS1):​n.1827C>T variant causes a non coding transcript exon 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 ENST00000435641.5 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.380
• Publications: 3 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=-0.91).
• 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 rank	MANE	Protein	UniProt
LY86-AS1	NR_026970.1	n.927+4772C>T		intron_variant	Intron 6 of 7

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LY86-AS1	ENST00000435641.5	n.1827C>T		non_coding_transcript_exon_variant	Exon 7 of 7	2
LY86-AS1	ENST00000658580.1	n.1859C>T		non_coding_transcript_exon_variant	Exon 8 of 8
LY86-AS1	ENST00000665459.1	n.1579C>T		non_coding_transcript_exon_variant	Exon 7 of 7

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

African (AFR) AC: 0 AN: 0

American (AMR) AC: 0 AN: 0

Ashkenazi Jewish (ASJ) AC: 0 AN: 0

East Asian (EAS) AC: 0 AN: 0

South Asian (SAS) AC: 0 AN: 0

European-Finnish (FIN) AC: 0 AN: 0

Middle Eastern (MID) AC: 0 AN: 0

European-Non Finnish (NFE) AF: 0.500 AC: 1 AN: 2

Other (OTH) AC: 0 AN: 0

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

African (AFR) AF: 0.250 AC: 10388 AN: 41488

American (AMR) AF: 0.103 AC: 1569 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.140 AC: 487 AN: 3470

East Asian (EAS) AF: 0.00154 AC: 8 AN: 5180

South Asian (SAS) AF: 0.125 AC: 604 AN: 4822

European-Finnish (FIN) AF: 0.141 AC: 1486 AN: 10568

Middle Eastern (MID) AF: 0.241 AC: 71 AN: 294

European-Non Finnish (NFE) AF: 0.144 AC: 9788 AN: 67996

Other (OTH) AF: 0.151 AC: 318 AN: 2106

Alfa AF: 0.148 Hom.: 3252

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
PhyloP100		-0.38

Splicing

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

Other links and lift over

dbSNP: rs7774436; hg19: chr6-6361816;