6-31711688-G-C

Variant names:

• chr6-31711688-G-C
• rs805285
• ENST00000503322.1:c.802+1507G>C

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+1507G>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.354 in 224,204 control chromosomes in the GnomAD database, including 16,718 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 0.39 (13582 hom., cov: 30)
  • Exomes 𝑓: 0.27 (3136 hom.)
• Consequence: LY6G6F-LY6G6D ENST00000503322.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.231
• Publications: 21 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=-0.91).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.623 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000503322.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LY6G6F-LY6G6D	NM_001353334.2		c.802+1507G>C		intron	N/A	NP_001340263.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LY6G6F-LY6G6D	ENST00000503322.1	TSL:1	c.802+1507G>C		intron	N/A	ENSP00000421232.1
	ENSG00000204422	ENST00000461287.1	TSL:2	n.537+329C>G		intron	N/A
	ENSG00000293479	ENST00000697727.1		n.*83C>G		downstream_gene	N/A

Frequencies

GnomAD3 genomes AF: 0.394 AC: 59689 AN: 151660 Hom.: 13550 Cov.: 30

Gnomad AFR AF: 0.630

Gnomad AMI AF: 0.209

Gnomad AMR AF: 0.401

Gnomad ASJ AF: 0.310

Gnomad EAS AF: 0.390

Gnomad SAS AF: 0.440

Gnomad FIN AF: 0.402

Gnomad MID AF: 0.424

Gnomad NFE AF: 0.250

Gnomad OTH AF: 0.407

GnomAD4 exome AF: 0.269 AC: 19501 AN: 72426 Hom.: 3136 AF XY: 0.275 AC XY: 10674 AN XY: 38780

African (AFR) AF: 0.601 AC: 1106 AN: 1840

American (AMR) AF: 0.385 AC: 1570 AN: 4076

Ashkenazi Jewish (ASJ) AF: 0.290 AC: 598 AN: 2064

East Asian (EAS) AF: 0.344 AC: 1151 AN: 3344

South Asian (SAS) AF: 0.377 AC: 3666 AN: 9712

European-Finnish (FIN) AF: 0.317 AC: 861 AN: 2720

Middle Eastern (MID) AF: 0.293 AC: 78 AN: 266

European-Non Finnish (NFE) AF: 0.211 AC: 9400 AN: 44480

Other (OTH) AF: 0.273 AC: 1071 AN: 3924

GnomAD4 genome AF: 0.394 AC: 59771 AN: 151778 Hom.: 13582 Cov.: 30 AF XY: 0.402 AC XY: 29797 AN XY: 74162

African (AFR) AF: 0.630 AC: 26027 AN: 41334

American (AMR) AF: 0.402 AC: 6126 AN: 15256

Ashkenazi Jewish (ASJ) AF: 0.310 AC: 1074 AN: 3466

East Asian (EAS) AF: 0.390 AC: 2008 AN: 5144

South Asian (SAS) AF: 0.440 AC: 2115 AN: 4810

European-Finnish (FIN) AF: 0.402 AC: 4231 AN: 10530

Middle Eastern (MID) AF: 0.418 AC: 123 AN: 294

European-Non Finnish (NFE) AF: 0.250 AC: 17014 AN: 67932

Other (OTH) AF: 0.411 AC: 863 AN: 2102

Alfa AF: 0.152 Hom.: 254

Bravo AF: 0.404

Asia WGS AF: 0.503 AC: 1743 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	5.4
DANN	Benign	0.28
PhyloP100		0.23
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: rs805285; hg19: chr6-31679465;