15-23440775-C-CCCGCATCTTCTCCTCCTGCTT

Variant summary

Our verdict is Uncertain significance. Variant got 2 ACMG points: 2P and 0B. PM4

The NM_001304388.2(GOLGA6L2):c.1699_1700insAAGCAGGAGGAGAAGATGCGG(p.Ala566_Gly567insGluAlaGlyGlyGluAspAla) variant causes a inframe insertion change involving the alteration of a non-conserved nucleotide. Variant has been reported in ClinVar as Uncertain significance (no stars).

• Frequency:
  • Genomes: 𝑓 0.47 (1 hom., cov: 0)
  • Exomes 𝑓: 0.45 (49 hom.)
  • Failed GnomAD Quality Control
• Consequence: GOLGA6L2 NM_001304388.2 inframe_insertion
• Clinical Significance: Uncertain significance no assertion criteria provided U:1
• Conservation: PhyloP100: -0.405

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 2 ACMG points.

• PM4: Nonframeshift variant in NON repetitive region in NM_001304388.2.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
GOLGA6L2	NM_001304388.2	c.1699_1700insAAGCAGGAGGAGAAGATGCGG	p.Ala566_Gly567insGluAlaGlyGlyGluAspAla	inframe_insertion	8/8	ENST00000567107.6
GOLGA6L2	XM_047432396.1	c.1540_1541insAAGCAGGAGGAGAAGATGCGG	p.Ala513_Gly514insGluAlaGlyGlyGluAspAla	inframe_insertion	6/6
GOLGA6L2	XM_047432397.1	c.1228-250_1228-249insAAGCAGGAGGAGAAGATGCGG		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
GOLGA6L2	ENST00000567107.6	c.1699_1700insAAGCAGGAGGAGAAGATGCGG	p.Ala566_Gly567insGluAlaGlyGlyGluAspAla	inframe_insertion	8/8	5	NM_001304388.2	P1
GOLGA6L2	ENST00000566571.5	c.*980_*981insAAGCAGGAGGAGAAGATGCGG		3_prime_UTR_variant, NMD_transcript_variant	7/7	5

Frequencies

GnomAD3 genomes AF: 0.00 AC: 66768 AN: 141536 Hom.: 1 Cov.: 0 FAILED QC

Gnomad AFR AF: 0.426

Gnomad AMI AF: 0.493

Gnomad AMR AF: 0.487

Gnomad ASJ AF: 0.487

Gnomad EAS AF: 0.484

Gnomad SAS AF: 0.480

Gnomad FIN AF: 0.492

Gnomad MID AF: 0.486

Gnomad NFE AF: 0.488

Gnomad OTH AF: 0.483

GnomAD4 exome Data not reliable, filtered out with message: AS_VQSR;InbreedingCoeff AF: 0.446 AC: 423941 AN: 950718 Hom.: 49 Cov.: 98 AF XY: 0.450 AC XY: 216152 AN XY: 480832

Gnomad4 AFR exome AF: 0.373

Gnomad4 AMR exome AF: 0.482

Gnomad4 ASJ exome AF: 0.471

Gnomad4 EAS exome AF: 0.480

Gnomad4 SAS exome AF: 0.468

Gnomad4 FIN exome AF: 0.488

Gnomad4 NFE exome AF: 0.439

Gnomad4 OTH exome AF: 0.454

GnomAD4 genome Data not reliable, filtered out with message: InbreedingCoeff AF: 0.472 AC: 66815 AN: 141648 Hom.: 1 Cov.: 0 AF XY: 0.471 AC XY: 32748 AN XY: 69464

Gnomad4 AFR AF: 0.426

Gnomad4 AMR AF: 0.487

Gnomad4 ASJ AF: 0.487

Gnomad4 EAS AF: 0.484

Gnomad4 SAS AF: 0.480

Gnomad4 FIN AF: 0.492

Gnomad4 NFE AF: 0.488

Gnomad4 OTH AF: 0.485

Alfa AF: 0.172 Hom.: 0

ClinVar

Significance: Uncertain significance

Submissions summary: Uncertain:1

Revision: no assertion criteria provided

Submissions by phenotype

not provided Uncertain:1

Uncertain significance, no assertion criteria provided

clinical testing

Department of Pathology and Laboratory Medicine, Sinai Health System

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Computational scores

Source: dbNSFP v4.3

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Other links and lift over

dbSNP: rs748500078; hg19: chr15-23685922;