15-23443797-A-T

Variant names:

• chr15-23443797-A-T
• rs4778531
• NM_001304388.2:c.571T>A

Variant summary

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

The NM_001304388.2(GOLGA6L2):​c.571T>A​(p.Trp191Arg) 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. 15/20 in silico tools predict a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency:
  • Genomes: not found (cov: 33)
  • Exomes 𝑓: 0.0 (0 hom.)
  • Failed GnomAD Quality Control
• Consequence: GOLGA6L2 NM_001304388.2 missense
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.132
• Publications: 11 publications found

Genes affected

GOLGA6L2 (HGNC:26695): (golgin A6 family like 2) Predicted to be located in cis-Golgi network. [provided by Alliance of Genome Resources, Apr 2022]

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=0.07401493).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
GOLGA6L2	NM_001304388.2	c.571T>A	p.Trp191Arg	missense_variant	Exon 5 of 8	ENST00000567107.6	NP_001291317.1
GOLGA6L2	XM_047432396.1	c.412T>A	p.Trp138Arg	missense_variant	Exon 3 of 6		XP_047288352.1
GOLGA6L2	XM_047432397.1	c.571T>A	p.Trp191Arg	missense_variant	Exon 5 of 11		XP_047288353.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
GOLGA6L2	ENST00000567107.6	c.571T>A	p.Trp191Arg	missense_variant	Exon 5 of 8	5	NM_001304388.2	ENSP00000454407.1
GOLGA6L2	ENST00000566571.5	n.541T>A		non_coding_transcript_exon_variant	Exon 4 of 7	5		ENSP00000456523.1

Frequencies

GnomAD3 genomes Cov.: 33

GnomAD4 exome Data not reliable, filtered out with message: AC0;AS_VQSR AF: 0.00 AC: 0 AN: 1386514 Hom.: 0 Cov.: 44 AF XY: 0.00 AC XY: 0 AN XY: 684400

African (AFR) AF: 0.00 AC: 0 AN: 31662

American (AMR) AF: 0.00 AC: 0 AN: 35984

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 25178

East Asian (EAS) AF: 0.00 AC: 0 AN: 35888

South Asian (SAS) AF: 0.00 AC: 0 AN: 79342

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 34240

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 5698

European-Non Finnish (NFE) AF: 0.00 AC: 0 AN: 1080366

Other (OTH) AF: 0.00 AC: 0 AN: 58156

GnomAD4 genome Cov.: 33

Alfa AF: 0.00 Hom.: 111235

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Benign	0.10
BayesDel_addAF	Benign	-0.36	T
BayesDel_noAF	Benign	-0.76
CADD	Benign	1.2
DANN	Benign	0.70
DEOGEN2	Benign	0.0011	T;.
Eigen	Benign	-1.5
Eigen_PC	Benign	-1.7
FATHMM_MKL	Benign	0.0013	N
LIST_S2	Benign	0.023	T;T
M_CAP	Benign	0.0010	T
MetaRNN	Benign	0.074	T;T
MetaSVM	Benign	-0.99	T
MutationAssessor	Benign	0.0	N;.
PhyloP100		0.13
PrimateAI	Uncertain	0.54	T
PROVEAN	Benign	2.2	N;.
REVEL	Benign	0.033
Sift4G	Benign	0.33	T;T
Polyphen		0.020	B;.
Vest4		0.092
MutPred		0.42		Gain of disorder (P = 0.0022);.;
MVP		0.040
MPC		0.015
ClinPred		0.068	T
Varity_R		0.11
gMVP		0.089
Mutation Taster		=100/0	polymorphism

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: rs4778531; hg19: chr15-23688944;