dbSNP rs748500078: GOLGA6L2:p.Ala566_Gly567insValAlaGlyGlyGluAspAla (chr15-23440775-C-CCCGCATCTTCTCCTCCTGCTA) – ACMG Classification: Uncertain_significance (2 pts)

Variant summary

Our verdict is Uncertain significance. The variant received 2 ACMG points: 2P and 0B. PM4

The NM_001304388.2(GOLGA6L2):c.1699_1700insTAGCAGGAGGAGAAGATGCGG(p.Ala566_Gly567insValAlaGlyGlyGluAspAla) variant causes a conservative inframe insertion change involving the alteration of a non-conserved nucleotide. It is difficult to determine the true allele frequency of this variant because it is of type INS_BIG, and the frequency of such variant types in population databases may be underestimated and unreliable. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: not found (cov: 0)

Exomes 𝑓: 0.0 ( 0 hom. )

Failed GnomAD Quality Control

Consequence

GOLGA6L2
NM_001304388.2 conservative_inframe_insertion

Scores

Not classified

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.405

Publications

0 publications found

Variant links:

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]

GOLGA6L2 links:

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ACMG classification

Classification was made for transcript

Our verdict: Uncertain_significance. The variant received 2 ACMG points.

PM4

Nonframeshift variant in NON repetitive region in NM_001304388.2.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001304388.2. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	GOLGA6L2	NM_001304388.2	MANE Select	c.1699_1700insTAGCAGGAGGAGAAGATGCGG	p.Ala566_Gly567insValAlaGlyGlyGluAspAla	conservative_inframe_insertion	Exon 8 of 8	NP_001291317.1	Q8N9W4-3

Ensembl Transcripts

Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
GOLGA6L2	ENST00000567107.6	TSL:5 MANE Select	c.1699_1700insTAGCAGGAGGAGAAGATGCGG	p.Ala566_Gly567insValAlaGlyGlyGluAspAla	conservative_inframe_insertion	Exon 8 of 8	ENSP00000454407.1	Q8N9W4-3
GOLGA6L2	ENST00000566571.5	TSL:5	n.980_981insTAGCAGGAGGAGAAGATGCGG		non_coding_transcript_exon	Exon 7 of 7	ENSP00000456523.1	H3BS38
GOLGA6L2	ENST00000566571.5	TSL:5	n.980_981insTAGCAGGAGGAGAAGATGCGG		3_prime_UTR	Exon 7 of 7	ENSP00000456523.1	H3BS38

Frequencies

GnomAD3 genomes

Cov.:

GnomAD4 exome

Data not reliable, filtered out with message: AC0;AS_VQSR

AF:

0.00

AC:

AN:

1287450

Hom.:

Cov.:

AF XY:

0.00

AC XY:

AN XY:

638974

African (AFR)

AF:

0.00

AC:

AN:

29352

American (AMR)

AF:

0.00

AC:

AN:

35400

Ashkenazi Jewish (ASJ)

AF:

0.00

AC:

AN:

24384

East Asian (EAS)

AF:

0.00

AC:

AN:

35026

South Asian (SAS)

AF:

0.00

AC:

AN:

76830

European-Finnish (FIN)

AF:

0.00

AC:

AN:

42138

Middle Eastern (MID)

AF:

0.00

AC:

AN:

5496

European-Non Finnish (NFE)

AF:

0.00

AC:

AN:

984472

Other (OTH)

AF:

0.00

AC:

AN:

54352

GnomAD4 genome

Cov.:

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

PhyloP100

-0.41

Splicing

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

Publications

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Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Variant Effect in Transcripts

RefSeq Transcripts

Ensembl Transcripts

Frequencies

ClinVar

Computational scores

Splicing

Publications

Other links and lift over