chr15-23440461-T-A

Variant names:

• chr15-23440461-T-A
• NM_001304388.2:c.2014A>T

Variant summary

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

The NM_001304388.2(GOLGA6L2):​c.2014A>T​(p.Arg672*) variant causes a stop gained change involving the alteration of a non-conserved nucleotide. In-silico tool predicts a pathogenic outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency:
  • Genomes: not found (cov: 0)
  • Exomes 𝑓: 0.000015 (0 hom.)
  • Failed GnomAD Quality Control
• Consequence: GOLGA6L2 NM_001304388.2 stop_gained
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.17

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

Verdict is Uncertain_significance. Variant got 0 ACMG points.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
GOLGA6L2	NM_001304388.2	c.2014A>T	p.Arg672*	stop_gained	Exon 8 of 8	ENST00000567107.6	NP_001291317.1
GOLGA6L2	XM_047432396.1	c.1855A>T	p.Arg619*	stop_gained	Exon 6 of 6		XP_047288352.1
GOLGA6L2	XM_047432397.1	c.1293A>T	p.Glu431Asp	missense_variant	Exon 10 of 11		XP_047288353.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
GOLGA6L2	ENST00000567107.6	c.2014A>T	p.Arg672*	stop_gained	Exon 8 of 8	5	NM_001304388.2	ENSP00000454407.1
GOLGA6L2	ENST00000566571.5	n.*1295A>T		non_coding_transcript_exon_variant	Exon 7 of 7	5		ENSP00000456523.1
GOLGA6L2	ENST00000566571.5	n.*1295A>T		3_prime_UTR_variant	Exon 7 of 7	5		ENSP00000456523.1

Frequencies

GnomAD3 genomes Cov.: 0

GnomAD4 exome Data not reliable, filtered out with message: AS_VQSR AF: 0.0000150 AC: 3 AN: 200556 Hom.: 0 Cov.: 0 AF XY: 0.00000991 AC XY: 1 AN XY: 100872

Gnomad4 AFR exome AF: 0.000158

Gnomad4 AMR exome AF: 0.00

Gnomad4 ASJ exome AF: 0.00

Gnomad4 EAS exome AF: 0.00

Gnomad4 SAS exome AF: 0.00

Gnomad4 FIN exome AF: 0.00

Gnomad4 NFE exome AF: 0.0000131

Gnomad4 OTH exome AF: 0.00

GnomAD4 genome Cov.: 0

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_addAF	Pathogenic	0.16	D
BayesDel_noAF	Uncertain	-0.010
CADD	Pathogenic	27
DANN	Benign	0.95
FATHMM_MKL	Benign	0.0011	N
Vest4		0.0090

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: chr15-23685608;