rs2233128

Positions:

• chr6-6654666-G-A
• chr6-6654666-G-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BS1 BS2

The NM_004271.4(LY86):​c.*39G>A variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00112 in 1,549,500 control chromosomes in the GnomAD database, including 21 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 0.0012 (3 hom., cov: 33)
  • Exomes 𝑓: 0.0011 (18 hom.)
• Consequence: LY86 NM_004271.4 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.81

Genes affected

LY86 (HGNC:16837): (lymphocyte antigen 86) Acts upstream of or within positive regulation of lipopolysaccharide-mediated signaling pathway. Predicted to be located in extracellular space. [provided by Alliance of Genome Resources, Apr 2022]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BS1: Variant frequency is greater than expected in population eas. gnomad4 allele frequency = 0.00121 (185/152266) while in subpopulation EAS AF= 0.023 (119/5172). AF 95% confidence interval is 0.0197. There are 3 homozygotes in gnomad4. There are 97 alleles in male gnomad4 subpopulation. Median coverage is 33. This position pass quality control queck.
• BS2: High Homozygotes in GnomAd4 at 3 AR gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LY86	NM_004271.4	c.*39G>A		3_prime_UTR_variant	5/5	ENST00000230568.5	NP_004262.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
LY86	ENST00000230568.5	c.*39G>A		3_prime_UTR_variant	5/5	1	NM_004271.4	ENSP00000230568	P1
LY86	ENST00000379953.6	c.*39G>A		3_prime_UTR_variant	6/6	5		ENSP00000369286	P1

Frequencies

GnomAD3 genomes AF: 0.00122 AC: 186 AN: 152148 Hom.: 3 Cov.: 33

Gnomad AFR AF: 0.000290

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.00151

Gnomad ASJ AF: 0.00

Gnomad EAS AF: 0.0231

Gnomad SAS AF: 0.00270

Gnomad FIN AF: 0.00

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.000235

Gnomad OTH AF: 0.000955

GnomAD3 exomes AF: 0.00230 AC: 572 AN: 248174 Hom.: 9 AF XY: 0.00224 AC XY: 300 AN XY: 133926

Gnomad AFR exome AF: 0.000311

Gnomad AMR exome AF: 0.000996

Gnomad ASJ exome AF: 0.00

Gnomad EAS exome AF: 0.0257

Gnomad SAS exome AF: 0.00114

Gnomad FIN exome AF: 0.00

Gnomad NFE exome AF: 0.000169

Gnomad OTH exome AF: 0.00182

GnomAD4 exome AF: 0.00111 AC: 1545 AN: 1397234 Hom.: 18 Cov.: 22 AF XY: 0.00107 AC XY: 749 AN XY: 698766

Gnomad4 AFR exome AF: 0.0000936

Gnomad4 AMR exome AF: 0.000831

Gnomad4 ASJ exome AF: 0.0000390

Gnomad4 EAS exome AF: 0.0262

Gnomad4 SAS exome AF: 0.00117

Gnomad4 FIN exome AF: 0.0000188

Gnomad4 NFE exome AF: 0.000198

Gnomad4 OTH exome AF: 0.00268

GnomAD4 genome AF: 0.00121 AC: 185 AN: 152266 Hom.: 3 Cov.: 33 AF XY: 0.00130 AC XY: 97 AN XY: 74430

Gnomad4 AFR AF: 0.000289

Gnomad4 AMR AF: 0.00150

Gnomad4 ASJ AF: 0.00

Gnomad4 EAS AF: 0.0230

Gnomad4 SAS AF: 0.00270

Gnomad4 FIN AF: 0.00

Gnomad4 NFE AF: 0.000235

Gnomad4 OTH AF: 0.000945

Alfa AF: 0.000295 Hom.: 0

Bravo AF: 0.00107

Asia WGS AF: 0.0180 AC: 63 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	0.047
DANN	Benign	0.40

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

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

Publications

LitVar

Other links and lift over

dbSNP: rs2233128; hg19: chr6-6654899; COSMIC: COSV57911935; COSMIC: COSV57911935;