6-31710251-C-T

Variant names:

• chr6-31710251-C-T
• rs805288
• NM_001003693.3:c.802+70C>T

Variant summary

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

The NM_001003693.3(LY6G6F):​c.802+70C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.285 in 1,610,490 control chromosomes in the GnomAD database, including 69,787 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 0.37 (11187 hom., cov: 31)
  • Exomes 𝑓: 0.28 (58600 hom.)
• Consequence: LY6G6F NM_001003693.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.09
• Publications: 8 publications found

Genes affected

LY6G6F (HGNC:13933): (lymphocyte antigen 6 family member G6F) The human G6f protein is a type I transmembrane protein belonging to the immunoglobin (Ig) superfamily, which is comprised of cell-surface proteins involved in the immune system and cellular recognition (de Vet et al., 2003 [PubMed 12852788]).[supplied by OMIM, Mar 2008]

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=-0.92).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.542 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LY6G6F	NM_001003693.3	c.802+70C>T		intron_variant	Intron 4 of 5	ENST00000375832.5	NP_001003693.1
LY6G6F-LY6G6D	NM_001353334.2	c.802+70C>T		intron_variant	Intron 4 of 5		NP_001340263.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LY6G6F	ENST00000375832.5	c.802+70C>T		intron_variant	Intron 4 of 5	1	NM_001003693.3	ENSP00000364992.5
LY6G6F-LY6G6D	ENST00000503322.1	c.802+70C>T		intron_variant	Intron 4 of 5	1		ENSP00000421232.1
ENSG00000204422	ENST00000461287.1	n.537+1766G>A		intron_variant	Intron 3 of 21	2

Frequencies

GnomAD3 genomes AF: 0.365 AC: 55484 AN: 151818 Hom.: 11179 Cov.: 31

Gnomad AFR AF: 0.548

Gnomad AMI AF: 0.256

Gnomad AMR AF: 0.279

Gnomad ASJ AF: 0.303

Gnomad EAS AF: 0.323

Gnomad SAS AF: 0.354

Gnomad FIN AF: 0.418

Gnomad MID AF: 0.386

Gnomad NFE AF: 0.275

Gnomad OTH AF: 0.363

GnomAD4 exome AF: 0.276 AC: 402789 AN: 1458554 Hom.: 58600 Cov.: 37 AF XY: 0.277 AC XY: 200683 AN XY: 725262

African (AFR) AF: 0.551 AC: 18409 AN: 33432

American (AMR) AF: 0.243 AC: 10868 AN: 44656

Ashkenazi Jewish (ASJ) AF: 0.308 AC: 8003 AN: 25978

East Asian (EAS) AF: 0.312 AC: 12359 AN: 39658

South Asian (SAS) AF: 0.330 AC: 28439 AN: 86128

European-Finnish (FIN) AF: 0.395 AC: 20640 AN: 52218

Middle Eastern (MID) AF: 0.355 AC: 2045 AN: 5756

European-Non Finnish (NFE) AF: 0.256 AC: 284050 AN: 1110430

Other (OTH) AF: 0.298 AC: 17976 AN: 60298

GnomAD4 genome AF: 0.365 AC: 55527 AN: 151936 Hom.: 11187 Cov.: 31 AF XY: 0.370 AC XY: 27438 AN XY: 74252

African (AFR) AF: 0.548 AC: 22692 AN: 41446

American (AMR) AF: 0.279 AC: 4254 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.303 AC: 1050 AN: 3468

East Asian (EAS) AF: 0.323 AC: 1660 AN: 5140

South Asian (SAS) AF: 0.353 AC: 1699 AN: 4812

European-Finnish (FIN) AF: 0.418 AC: 4404 AN: 10546

Middle Eastern (MID) AF: 0.384 AC: 113 AN: 294

European-Non Finnish (NFE) AF: 0.275 AC: 18657 AN: 67932

Other (OTH) AF: 0.362 AC: 765 AN: 2114

Alfa AF: 0.318 Hom.: 2464

Bravo AF: 0.364

Asia WGS AF: 0.343 AC: 1189 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.30
DANN	Benign	0.74
PhyloP100		-1.1
Mutation Taster		=100/0	polymorphism (auto)

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.030		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: rs805288; hg19: chr6-31678028; COSMIC: COSV65442887; COSMIC: COSV65442887;