6-31678621-C-A

Variant names:

• chr6-31678621-C-A
• rs2280800
• NM_025262.4:c.289+480G>T

Variant summary

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

The NM_025262.4(LY6G5C):​c.289+480G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.135 in 152,062 control chromosomes in the GnomAD database, including 1,739 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 0.14 (1739 hom., cov: 32)
• Consequence: LY6G5C NM_025262.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.578
• Publications: 38 publications found

Genes affected

LY6G5C (HGNC:13932): (lymphocyte antigen 6 family member G5C) LY6G5C belongs to a cluster of leukocyte antigen-6 (LY6) genes located in the major histocompatibility complex (MHC) class III region on chromosome 6. Members of the LY6 superfamily typically contain 70 to 80 amino acids, including 8 to 10 cysteines. Most LY6 proteins are attached to the cell surface by a glycosylphosphatidylinositol (GPI) anchor that is directly involved in signal transduction (Mallya et al., 2002 [PubMed 12079290]).[supplied by OMIM, Mar 2008]

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 (AMR) allele frequency at 95% confidence interval = 0.183 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LY6G5C	NM_025262.4	c.289+480G>T		intron_variant	Intron 2 of 2	ENST00000383237.5	NP_079538.3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LY6G5C	ENST00000383237.5	c.289+480G>T		intron_variant	Intron 2 of 2	1	NM_025262.4	ENSP00000372724.4

Frequencies

GnomAD3 genomes AF: 0.135 AC: 20574 AN: 151944 Hom.: 1735 Cov.: 32

Gnomad AFR AF: 0.0808

Gnomad AMI AF: 0.134

Gnomad AMR AF: 0.188

Gnomad ASJ AF: 0.0300

Gnomad EAS AF: 0.146

Gnomad SAS AF: 0.104

Gnomad FIN AF: 0.330

Gnomad MID AF: 0.0443

Gnomad NFE AF: 0.135

Gnomad OTH AF: 0.105

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

GnomAD4 genome AF: 0.135 AC: 20597 AN: 152062 Hom.: 1739 Cov.: 32 AF XY: 0.144 AC XY: 10685 AN XY: 74324

African (AFR) AF: 0.0808 AC: 3352 AN: 41490

American (AMR) AF: 0.189 AC: 2889 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.0300 AC: 104 AN: 3472

East Asian (EAS) AF: 0.147 AC: 758 AN: 5174

South Asian (SAS) AF: 0.104 AC: 503 AN: 4830

European-Finnish (FIN) AF: 0.330 AC: 3476 AN: 10548

Middle Eastern (MID) AF: 0.0476 AC: 14 AN: 294

European-Non Finnish (NFE) AF: 0.135 AC: 9159 AN: 67962

Other (OTH) AF: 0.105 AC: 220 AN: 2102

Alfa AF: 0.131 Hom.: 5909

Bravo AF: 0.125

Asia WGS AF: 0.140 AC: 487 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	7.7
DANN	Benign	0.65
PhyloP100		-0.58
Mutation Taster		=100/0	polymorphism (auto)

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.14		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: rs2280800; hg19: chr6-31646398;