chr6-31710953-A-G

Variant names:

• chr6-31710953-A-G
• rs805287
• ENST00000503322.1:c.802+772A>G

Variant summary

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

The NM_001353334.2(LY6G6F-LY6G6D):​c.802+772A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.409 in 151,678 control chromosomes in the GnomAD database, including 13,969 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 (13969 hom., cov: 30)
• Consequence: LY6G6F-LY6G6D NM_001353334.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.488
• Publications: 31 publications found

Genes affected

LY6G6F-LY6G6D (HGNC:38821): (LY6G6F-LY6G6D readthrough) This locus represents naturally occurring readthrough transcription between the neighboring LY6G6F (lymphocyte antigen 6 family member G6F) and LY6G6D (lymphocyte antigen 6 family member G6D) genes on chromosome 6. The readthrough transcript encodes a fusion protein that shares sequence identity with each individual gene product. [provided by RefSeq, Jul 2017]

ENSG00000204422 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.603 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001353334.2. 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
	LY6G6F-LY6G6D	NM_001353334.2		c.802+772A>G		intron	N/A	NP_001340263.1

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LY6G6F-LY6G6D	ENST00000503322.1	TSL:1	c.802+772A>G		intron	N/A	ENSP00000421232.1
	ENSG00000204422	ENST00000461287.1	TSL:2	n.537+1064T>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.409 AC: 61968 AN: 151560 Hom.: 13952 Cov.: 30

Gnomad AFR AF: 0.610

Gnomad AMI AF: 0.245

Gnomad AMR AF: 0.417

Gnomad ASJ AF: 0.326

Gnomad EAS AF: 0.412

Gnomad SAS AF: 0.433

Gnomad FIN AF: 0.420

Gnomad MID AF: 0.449

Gnomad NFE AF: 0.288

Gnomad OTH AF: 0.411

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

GnomAD4 genome AF: 0.409 AC: 62035 AN: 151678 Hom.: 13969 Cov.: 30 AF XY: 0.416 AC XY: 30809 AN XY: 74118

African (AFR) AF: 0.609 AC: 25147 AN: 41272

American (AMR) AF: 0.417 AC: 6369 AN: 15266

Ashkenazi Jewish (ASJ) AF: 0.326 AC: 1129 AN: 3466

East Asian (EAS) AF: 0.412 AC: 2118 AN: 5144

South Asian (SAS) AF: 0.433 AC: 2081 AN: 4808

European-Finnish (FIN) AF: 0.420 AC: 4417 AN: 10510

Middle Eastern (MID) AF: 0.449 AC: 131 AN: 292

European-Non Finnish (NFE) AF: 0.288 AC: 19545 AN: 67900

Other (OTH) AF: 0.415 AC: 875 AN: 2108

Alfa AF: 0.323 Hom.: 32796

Bravo AF: 0.417

Asia WGS AF: 0.490 AC: 1701 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	7.1
DANN	Benign	0.83
PhyloP100		0.49
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs805287; hg19: chr6-31678730;