rs6916278

Variant names:

• chr6-31710997-G-A
• rs6916278
• ENST00000503322.1:c.802+816G>A

Variant summary

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

The ENST00000503322.1(LY6G6F-LY6G6D):​c.802+816G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.077 in 152,016 control chromosomes in the GnomAD database, including 638 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 0.077 (638 hom., cov: 31)
• Consequence: LY6G6F-LY6G6D ENST00000503322.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.777
• Publications: 14 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=-0.89).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.137 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LY6G6F-LY6G6D	NM_001353334.2	c.802+816G>A		intron_variant	Intron 4 of 5		NP_001340263.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LY6G6F-LY6G6D	ENST00000503322.1	c.802+816G>A		intron_variant	Intron 4 of 5	1		ENSP00000421232.1
ENSG00000204422	ENST00000461287.1	n.537+1020C>T		intron_variant	Intron 3 of 21	2

Frequencies

GnomAD3 genomes AF: 0.0771 AC: 11712 AN: 151898 Hom.: 637 Cov.: 31

Gnomad AFR AF: 0.141

Gnomad AMI AF: 0.0274

Gnomad AMR AF: 0.0969

Gnomad ASJ AF: 0.0435

Gnomad EAS AF: 0.00270

Gnomad SAS AF: 0.00621

Gnomad FIN AF: 0.00500

Gnomad MID AF: 0.0411

Gnomad NFE AF: 0.0585

Gnomad OTH AF: 0.0831

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

GnomAD4 genome AF: 0.0770 AC: 11711 AN: 152016 Hom.: 638 Cov.: 31 AF XY: 0.0729 AC XY: 5421 AN XY: 74314

African (AFR) AF: 0.140 AC: 5804 AN: 41394

American (AMR) AF: 0.0969 AC: 1479 AN: 15266

Ashkenazi Jewish (ASJ) AF: 0.0435 AC: 151 AN: 3468

East Asian (EAS) AF: 0.00270 AC: 14 AN: 5178

South Asian (SAS) AF: 0.00601 AC: 29 AN: 4826

European-Finnish (FIN) AF: 0.00500 AC: 53 AN: 10606

Middle Eastern (MID) AF: 0.0374 AC: 11 AN: 294

European-Non Finnish (NFE) AF: 0.0585 AC: 3973 AN: 67968

Other (OTH) AF: 0.0817 AC: 172 AN: 2104

Alfa AF: 0.0637 Hom.: 949

Bravo AF: 0.0897

Asia WGS AF: 0.0110 AC: 39 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	7.3
DANN	Benign	0.45
PhyloP100		0.78
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: rs6916278; hg19: chr6-31678774;