rs805287

chr6-31710953-A-Gchr6-31710953-A-T

Variant summary

Our verdict is Benign. Variant got -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

Genes affected

LY6G6F-LY6G6D (HGNC:):

ACMG classification

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LY6G6F-LY6G6D	NM_001353334.2	c.802+772A>G		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt

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

Gnomad4 AFR AF: 0.609

Gnomad4 AMR AF: 0.417

Gnomad4 ASJ AF: 0.326

Gnomad4 EAS AF: 0.412

Gnomad4 SAS AF: 0.433

Gnomad4 FIN AF: 0.420

Gnomad4 NFE AF: 0.288

Gnomad4 OTH AF: 0.415

Alfa AF: 0.309 Hom.: 11336

Bravo AF: 0.417

Asia WGS AF: 0.490 AC: 1701 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
Cadd	Benign	7.1
Dann	Benign	0.83

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

Publications

LitVar

Other links and lift over

dbSNP: rs805287; hg19: chr6-31678730;