rs2908282

Positions:

• chr7-44209229-G-A
• chr7-44209229-G-C

Variant summary

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

The NM_006555.4(YKT6):​c.459+1031G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.195 in 152,088 control chromosomes in the GnomAD database, including 3,016 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 0.19 (3016 hom., cov: 33)
• Consequence: YKT6 NM_006555.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.915

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]

YKT6 (HGNC:):

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 (AMR) allele frequency at 95% confidence interval = 0.27 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
YKT6	NM_006555.4	c.459+1031G>A		intron_variant		ENST00000223369.3	NP_006546.1
YKT6	NM_001410874.1	c.459+1031G>A		intron_variant			NP_001397803.1
YKT6	NM_001363678.2	c.459+1031G>A		intron_variant			NP_001350607.1
YKT6	XM_054328423.1	c.459+1031G>A		intron_variant			XP_054184398.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
YKT6	ENST00000223369.3	c.459+1031G>A		intron_variant		1	NM_006555.4	ENSP00000223369.2

Frequencies

GnomAD3 genomes AF: 0.195 AC: 29609 AN: 151970 Hom.: 3011 Cov.: 33

Gnomad AFR AF: 0.231

Gnomad AMI AF: 0.268

Gnomad AMR AF: 0.276

Gnomad ASJ AF: 0.169

Gnomad EAS AF: 0.187

Gnomad SAS AF: 0.140

Gnomad FIN AF: 0.109

Gnomad MID AF: 0.263

Gnomad NFE AF: 0.171

Gnomad OTH AF: 0.229

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

GnomAD4 genome AF: 0.195 AC: 29634 AN: 152088 Hom.: 3016 Cov.: 33 AF XY: 0.193 AC XY: 14361 AN XY: 74342

Gnomad4 AFR AF: 0.231

Gnomad4 AMR AF: 0.277

Gnomad4 ASJ AF: 0.169

Gnomad4 EAS AF: 0.187

Gnomad4 SAS AF: 0.139

Gnomad4 FIN AF: 0.109

Gnomad4 NFE AF: 0.171

Gnomad4 OTH AF: 0.226

Alfa AF: 0.166 Hom.: 780

Bravo AF: 0.214

Asia WGS AF: 0.143 AC: 501 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	0.16
DANN	Benign	0.60

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: rs2908282; hg19: chr7-44248828;