rs201670904

Positions:

• chr15-82344706-C-G
• chr15-82344706-C-T

Variant summary

Our verdict is Uncertain significance. Variant got 1 ACMG points: 3P and 2B. PM2 PP2 BP4_Moderate

The NM_001164465.3(GOLGA6L10):​c.1154G>C​(p.Arg385Pro) 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. 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. R385Q) has been classified as Benign.

• Frequency: Genomes: not found (cov: 34)
• Consequence: GOLGA6L10 NM_001164465.3 missense
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.328

Genes affected

GOLGA6L10 (HGNC:37228): (golgin A6 family like 10)

ACMG classification

Verdict is Uncertain_significance. Variant got 1 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• PP2: Missense variant where missense usually causes diseases, GOLGA6L10
• BP4: Computational evidence support a benign effect (MetaRNN=0.13064721).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
GOLGA6L10	NM_001164465.3	c.1154G>C	p.Arg385Pro	missense_variant	6/9	ENST00000610657.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
GOLGA6L10	ENST00000610657.2	c.1154G>C	p.Arg385Pro	missense_variant	6/9	2	NM_001164465.3	P2
GOLGA6L10	ENST00000621197.4	c.905G>C	p.Arg302Pro	missense_variant	7/10	5		A2

Frequencies

GnomAD3 genomes Cov.: 34

GnomAD4 exome Cov.: 42

GnomAD4 genome Cov.: 34

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Uncertain	0.49
BayesDel_addAF	Benign	-0.26	T
BayesDel_noAF	Benign	-0.61
CADD	Benign	11
DANN	Benign	0.38
FATHMM_MKL	Benign	0.0031	N
LIST_S2	Benign	0.28	T;T;T
M_CAP	Benign	0.0032	T
MetaRNN	Benign	0.13	T;T;T
PrimateAI	Uncertain	0.52	T
Sift4G	Benign	0.19	T;T;T
Vest4		0.30
MVP		0.014
Varity_R		0.19
gMVP		0.20

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

LitVar

Other links and lift over

dbSNP: rs201670904; hg19: chr15-83013345;