dbSNP rs917793: YKT6:c.188-131A>T (chr7-44206254-A-T) – ACMG Classification: Benign (-12 pts)

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBA1

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

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -2.79

Publications

18 publications found

Variant links:

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 links:

Genome browser will be placed here

ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -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	Effect	Exon rank	MANE	Protein
YKT6	NM_006555.4 link	c.188-131A>T	intron_variant	Intron 2 of 6	ENST00000223369.3	NP_006546.1
YKT6	NM_001410874.1 link	c.188-131A>T	intron_variant	Intron 2 of 7		NP_001397803.1
YKT6	NM_001363678.2 link	c.188-131A>T	intron_variant	Intron 2 of 5		NP_001350607.1
YKT6	XM_054328423.1 link	c.188-131A>T	intron_variant	Intron 2 of 6		XP_054184398.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
YKT6	ENST00000223369.3 link	c.188-131A>T		intron_variant	Intron 2 of 6	1	NM_006555.4	ENSP00000223369.2

Frequencies

GnomAD3 genomes

AF:

0.211

AC:

32052

AN:

152016

Hom.:

3652

Cov.:

show subpopulations

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

show subpopulations

African (AFR)

AF:

0.283

AC:

5060

AN:

17888

American (AMR)

AF:

0.335

AC:

10466

AN:

31222

Ashkenazi Jewish (ASJ)

AF:

0.174

AC:

3081

AN:

17702

East Asian (EAS)

AF:

0.202

AC:

6523

AN:

32354

South Asian (SAS)

AF:

0.136

AC:

7843

AN:

57838

European-Finnish (FIN)

AF:

0.110

AC:

4292

AN:

38938

Middle Eastern (MID)

AF:

0.229

AC:

637

AN:

2778

European-Non Finnish (NFE)

AF:

0.172

AC:

79026

AN:

460558

Other (OTH)

AF:

0.189

AC:

6501

AN:

34388

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.503

Heterozygous variant carriers

5013

10026

15038

20051

25064

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

1752

3504

5256

7008

8760

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

GnomAD4 genome

AF:

0.211

AC:

32094

AN:

152134

Hom.:

3663

Cov.:

AF XY:

0.208

AC XY:

15492

AN XY:

74398

show subpopulations

African (AFR)

AF:

0.286

AC:

11880

AN:

41466

American (AMR)

AF:

0.283

AC:

4321

AN:

15292

Ashkenazi Jewish (ASJ)

AF:

0.169

AC:

587

AN:

3470

East Asian (EAS)

AF:

0.187

AC:

969

AN:

5180

South Asian (SAS)

AF:

0.139

AC:

669

AN:

4822

European-Finnish (FIN)

AF:

0.108

AC:

1150

AN:

10602

Middle Eastern (MID)

AF:

0.265

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.172

AC:

11692

AN:

67982

Other (OTH)

AF:

0.237

AC:

502

AN:

2114

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.503

Heterozygous variant carriers

1309

2618

3926

5235

6544

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

344

688

1032

1376

1720

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

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

(source)

DANN

Benign

0.57

PhyloP100

-2.8

Mutation Taster

=100/0

polymorphism (auto)

(source)

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

You must be logged in to view publications. This limit was set because tens of millions (!) of queries from AI bots are generated daily.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over