6-31711688-G-C

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+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 NM_001353334.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.231

Genes affected

LY6G6F-LY6G6D (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.623 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LY6G6F-LY6G6D	NM_001353334.2	c.802+1507G>C		intron_variant

Ensembl

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

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

Gnomad4 AFR exome AF: 0.601

Gnomad4 AMR exome AF: 0.385

Gnomad4 ASJ exome AF: 0.290

Gnomad4 EAS exome AF: 0.344

Gnomad4 SAS exome AF: 0.377

Gnomad4 FIN exome AF: 0.317

Gnomad4 NFE exome AF: 0.211

Gnomad4 OTH exome AF: 0.273

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

Gnomad4 AFR AF: 0.630

Gnomad4 AMR AF: 0.402

Gnomad4 ASJ AF: 0.310

Gnomad4 EAS AF: 0.390

Gnomad4 SAS AF: 0.440

Gnomad4 FIN AF: 0.402

Gnomad4 NFE AF: 0.250

Gnomad4 OTH AF: 0.411

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 v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
Cadd	Benign	5.4
Dann	Benign	0.28

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: rs805285; hg19: chr6-31679465;