7-44205764-A-G

Variant names:

• chr7-44205764-A-G
• rs10278336
• NM_006555.4:c.188-621A>G

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_006555.4(YKT6):​c.188-621A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.367 in 151,994 control chromosomes in the GnomAD database, including 10,892 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 0.37 (10892 hom., cov: 32)
• Consequence: YKT6 NM_006555.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.484
• Publications: 46 publications found

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

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.435 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_006555.4. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	YKT6	NM_006555.4	MANE Select	c.188-621A>G		intron	N/A	NP_006546.1
	YKT6	NM_001410874.1		c.188-621A>G		intron	N/A	NP_001397803.1
	YKT6	NM_001363678.2		c.188-621A>G		intron	N/A	NP_001350607.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	YKT6	ENST00000223369.3	TSL:1 MANE Select	c.188-621A>G		intron	N/A	ENSP00000223369.2
	YKT6	ENST00000677090.1		c.188-621A>G		intron	N/A	ENSP00000504160.1
	YKT6	ENST00000678359.1		c.188-621A>G		intron	N/A	ENSP00000503337.1

Frequencies

GnomAD3 genomes AF: 0.367 AC: 55707 AN: 151876 Hom.: 10886 Cov.: 32

Gnomad AFR AF: 0.220

Gnomad AMI AF: 0.246

Gnomad AMR AF: 0.361

Gnomad ASJ AF: 0.455

Gnomad EAS AF: 0.382

Gnomad SAS AF: 0.450

Gnomad FIN AF: 0.515

Gnomad MID AF: 0.320

Gnomad NFE AF: 0.426

Gnomad OTH AF: 0.345

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

GnomAD4 genome AF: 0.367 AC: 55725 AN: 151994 Hom.: 10892 Cov.: 32 AF XY: 0.374 AC XY: 27768 AN XY: 74304

African (AFR) AF: 0.219 AC: 9091 AN: 41448

American (AMR) AF: 0.360 AC: 5511 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.455 AC: 1569 AN: 3450

East Asian (EAS) AF: 0.381 AC: 1972 AN: 5170

South Asian (SAS) AF: 0.451 AC: 2172 AN: 4820

European-Finnish (FIN) AF: 0.515 AC: 5439 AN: 10564

Middle Eastern (MID) AF: 0.323 AC: 95 AN: 294

European-Non Finnish (NFE) AF: 0.426 AC: 28912 AN: 67938

Other (OTH) AF: 0.351 AC: 740 AN: 2110

Alfa AF: 0.329 Hom.: 4375

Bravo AF: 0.344

Asia WGS AF: 0.403 AC: 1401 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	2.8
DANN	Benign	0.75
PhyloP100		-0.48
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs10278336; hg19: chr7-44245363; COSMIC: COSV56272097; COSMIC: COSV56272097;