rs917793

chr7-44206254-A-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_006555.4(YKT6):c.188-131A>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.184 in 845,800 control chromosomes in the GnomAD database, including 15,636 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 0.21 (3663 hom., cov: 32)
  • Exomes 𝑓: 0.18 (11973 hom.)
• Consequence: YKT6 NM_006555.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.79

Genes affected

YKT6 (HGNC:16959): (YKT6 v-SNARE homolog) This gene product is one of the SNARE recognition molecules implicated in vesicular transport between secretory compartments. It is a membrane associated, isoprenylated protein that functions at the endoplasmic reticulum-Golgi transport step. This protein is highly conserved from yeast to human and can functionally complement the loss of the yeast homolog in the yeast secretory pathway. [provided by RefSeq, Jul 2008]

ACMG classification

Verdict is Benign. Variant got -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 = 0.282 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
YKT6	NM_006555.4	c.188-131A>T		intron_variant		ENST00000223369.3
YKT6	NM_001363678.2	c.188-131A>T		intron_variant
YKT6	NM_001410874.1	c.188-131A>T		intron_variant
YKT6	XM_054328423.1	c.188-131A>T		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
YKT6	ENST00000223369.3	c.188-131A>T		intron_variant		1	NM_006555.4	P1

Frequencies

GnomAD3 genomes AF: 0.211 AC: 32052 AN: 152016 Hom.: 3652 Cov.: 32

Gnomad AFR AF: 0.286

Gnomad AMI AF: 0.270

Gnomad AMR AF: 0.282

Gnomad ASJ AF: 0.169

Gnomad EAS AF: 0.187

Gnomad SAS AF: 0.140

Gnomad FIN AF: 0.108

Gnomad MID AF: 0.272

Gnomad NFE AF: 0.172

Gnomad OTH AF: 0.240

GnomAD4 exome AF: 0.178 AC: 123429 AN: 693666 Hom.: 11973 AF XY: 0.175 AC XY: 62730 AN XY: 359404

Gnomad4 AFR exome AF: 0.283

Gnomad4 AMR exome AF: 0.335

Gnomad4 ASJ exome AF: 0.174

Gnomad4 EAS exome AF: 0.202

Gnomad4 SAS exome AF: 0.136

Gnomad4 FIN exome AF: 0.110

Gnomad4 NFE exome AF: 0.172

Gnomad4 OTH exome AF: 0.189

GnomAD4 genome AF: 0.211 AC: 32094 AN: 152134 Hom.: 3663 Cov.: 32 AF XY: 0.208 AC XY: 15492 AN XY: 74398

Gnomad4 AFR AF: 0.286

Gnomad4 AMR AF: 0.283

Gnomad4 ASJ AF: 0.169

Gnomad4 EAS AF: 0.187

Gnomad4 SAS AF: 0.139

Gnomad4 FIN AF: 0.108

Gnomad4 NFE AF: 0.172

Gnomad4 OTH AF: 0.237

Alfa AF: 0.184 Hom.: 352

Bravo AF: 0.232

Asia WGS AF: 0.148 AC: 515 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	0.15
Dann	Benign	0.57

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: rs917793; hg19: chr7-44245853; COSMIC: COSV56272380; COSMIC: COSV56272380;