15-23129895-T-A

Variant names:

• chr15-23129895-T-A
• rs1595973664
• NM_001001413.3:c.1558A>T

Variant summary

Our verdict is Uncertain significance. The variant received 0 ACMG points: 2P and 2B. PM2 BP4_Moderate

The NM_001001413.3(GOLGA6L1):​c.1558A>T​(p.Arg520Trp) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. In-silico tool predicts a benign outcome for this variant. 6/7 in silico tools predict a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar. Another variant affecting the same amino acid position, but resulting in a different missense (i.e. R520G) has been classified as Uncertain significance.

• Frequency:
  • Genomes: not found (cov: 37)
  • Exomes 𝑓: 0.0 (0 hom.)
  • Failed GnomAD Quality Control
• Consequence: GOLGA6L1 NM_001001413.3 missense
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.26
• Publications: 0 publications found

Genes affected

GOLGA6L1 (HGNC:37444): (golgin A6 family like 1)

ACMG classification

Our verdict: Uncertain_significance. The variant received 0 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (MetaRNN=0.10900986).

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001001413.3. 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
	GOLGA6L1	NM_001001413.3	MANE Select	c.1558A>T	p.Arg520Trp	missense	Exon 8 of 9	NP_001001413.3	Q8N7Z2

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	GOLGA6L1	ENST00000614055.2	TSL:5 MANE Select	c.1558A>T	p.Arg520Trp	missense	Exon 8 of 9	ENSP00000478478.1	Q8N7Z2

Frequencies

GnomAD3 genomes Cov.: 37

GnomAD4 exome Data not reliable, filtered out with message: AC0;AS_VQSR AF: 0.00 AC: 0 AN: 779624 Hom.: 0 Cov.: 20 AF XY: 0.00 AC XY: 0 AN XY: 402810

African (AFR) AF: 0.00 AC: 0 AN: 22008

American (AMR) AF: 0.00 AC: 0 AN: 31430

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 19944

East Asian (EAS) AF: 0.00 AC: 0 AN: 30220

South Asian (SAS) AF: 0.00 AC: 0 AN: 61864

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 44968

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 3652

European-Non Finnish (NFE) AF: 0.00 AC: 0 AN: 529338

Other (OTH) AF: 0.00 AC: 0 AN: 36200

GnomAD4 genome Cov.: 37

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Benign	0.19
CADD	Benign	13
DANN	Benign	0.24
DEOGEN2	Benign	0.037	T
LIST_S2	Benign	0.85	D
MetaRNN	Benign	0.11	T
PhyloP100		-1.3
Sift4G	Uncertain	0.0070	D
Vest4		0.21
gMVP		0.027

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: rs1595973664;