chr15-82344740-G-T

Position:

• chr15-82344740-G-T

Variant summary

Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2 BP4_Moderate

The NM_001164465.3(GOLGA6L10):​c.1120C>A​(p.Gln374Lys) 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. 9/14 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).

• Frequency: Genomes: not found (cov: 34)
• Consequence: GOLGA6L10 NM_001164465.3 missense
• Clinical Significance: Uncertain significance criteria provided, single submitter U:1
• Conservation: PhyloP100: -1.79

Genes affected

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

ACMG classification

Verdict is Uncertain_significance. Variant got 0 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (MetaRNN=0.09066585).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
GOLGA6L10	NM_001164465.3	c.1120C>A	p.Gln374Lys	missense_variant	6/9	ENST00000610657.2	NP_001157937.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
GOLGA6L10	ENST00000610657.2	c.1120C>A	p.Gln374Lys	missense_variant	6/9	2	NM_001164465.3	ENSP00000479362.1
GOLGA6L10	ENST00000621197.4	c.871C>A	p.Gln291Lys	missense_variant	7/10	5		ENSP00000484254.2

Frequencies

GnomAD3 genomes Cov.: 34

GnomAD4 exome Cov.: 40

GnomAD4 genome Cov.: 34

ClinVar

Significance: Uncertain significance

Submissions summary: Uncertain:1

Revision: criteria provided, single submitter

Submissions by phenotype

not specified Uncertain:1

Uncertain significance, criteria provided, single submitter

clinical testing

Ambry Genetics

Feb 05, 2024

The c.1012C>A (p.L338M) alteration is located in exon 6 (coding exon 6) of the GOLGA6L10 gene. This alteration results from a C to A substitution at nucleotide position 1012, causing the leucine (L) at amino acid position 338 to be replaced by a methionine (M). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Benign	0.18
BayesDel_addAF	Benign	-0.24	T
BayesDel_noAF	Benign	-0.58
CADD	Benign	6.6
DANN	Benign	0.31
DEOGEN2	Benign	0.020	.;.;T
FATHMM_MKL	Benign	0.013	N
LIST_S2	Benign	0.58	T;T;T
M_CAP	Benign	0.0032	T
MetaRNN	Benign	0.091	T;T;T
PrimateAI	Uncertain	0.51	T
Sift4G	Benign	0.21	T;T;T
Vest4		0.085
MVP		0.014
Varity_R		0.19
gMVP		0.077

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

No publications associated with this variant yet.

Other links and lift over

hg19: chr15-83013379;