NM_001145004.2:c.1759A>T

Variant names:

• chr15-20534675-T-A
• rs1566840695
• NM_001145004.2:c.1759A>T

Variant summary

Our verdict is Uncertain significance. The variant received 2 ACMG points: 2P and 0B. PM2

The NM_001145004.2(GOLGA6L6):​c.1759A>T​(p.Lys587*) variant causes a stop gained change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. In-silico tool predicts a pathogenic outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar. Variant results in nonsense mediated mRNA decay.

• Frequency:
  • Genomes: 𝑓 0.0000089 (0 hom., cov: 22)
  • Failed GnomAD Quality Control
• Consequence: GOLGA6L6 NM_001145004.2 stop_gained
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -3.91
• Publications: 0 publications found

Genes affected

GOLGA6L6 (HGNC:37225): (golgin A6 family like 6)

ENSG00000294965 (HGNC:):

ACMG classification

Our verdict: Uncertain_significance. The variant received 2 ACMG points.

• PM2: Very rare variant in population databases, with high coverage

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001145004.2. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	GOLGA6L6	NM_001145004.2	MANE Select	c.1759A>T	p.Lys587*	stop_gained	Exon 8 of 9	NP_001138476.2	A8MZA4

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	GOLGA6L6	ENST00000619213.1	TSL:5 MANE Select	c.1759A>T	p.Lys587*	stop_gained	Exon 8 of 9	ENSP00000480376.1	A8MZA4
	ENSG00000294965	ENST00000727099.1		n.182+4022T>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.00000888 AC: 1 AN: 112656 Hom.: 0 Cov.: 22

Gnomad AFR AF: 0.0000328

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.00

Gnomad ASJ AF: 0.00

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.00

Gnomad FIN AF: 0.00

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.00

Gnomad OTH AF: 0.00

GnomAD4 exome Cov.: 23

GnomAD4 genome Data not reliable, filtered out with message: AS_VQSR AF: 0.00000887 AC: 1 AN: 112744 Hom.: 0 Cov.: 22 AF XY: 0.0000181 AC XY: 1 AN XY: 55150

African (AFR) AF: 0.0000327 AC: 1 AN: 30564

American (AMR) AF: 0.00 AC: 0 AN: 10976

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 2562

East Asian (EAS) AF: 0.00 AC: 0 AN: 3474

South Asian (SAS) AF: 0.00 AC: 0 AN: 3526

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 8318

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 232

European-Non Finnish (NFE) AF: 0.00 AC: 0 AN: 50840

Other (OTH) AF: 0.00 AC: 0 AN: 1566

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_addAF	Pathogenic	0.45	D
BayesDel_noAF	Pathogenic	0.41
CADD	Uncertain	24
DANN	Uncertain	0.99
Eigen	Benign	-0.31
Eigen_PC	Benign	-0.76
FATHMM_MKL	Benign	0.014	N
PhyloP100		-3.9
Vest4		0.021
Mutation Taster		=163/37	disease causing (fs/PTC)

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: rs1566840695; hg19: chr15-20739913;