Genetic Variant GOLGA6L22:p.Glu466Lys (chr15-22465656-G-A) – ACMG Classification: Likely_benign (-2 pts)

Variant summary

Our verdict is Likely benign. The variant received -2 ACMG points: 0P and 2B. BP4_Moderate

The NM_001396956.1(GOLGA6L22):c.1396G>A(p.Glu466Lys) variant causes a missense change involving the alteration of a non-conserved nucleotide. In-silico tool predicts a benign outcome for this variant. 12/17 in silico tools predict a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: 𝑓 0.0 ( 0 hom., cov: 6)

Exomes 𝑓: 0.000021 ( 1 hom. )

Failed GnomAD Quality Control

Consequence

GOLGA6L22
NM_001396956.1 missense

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -1.82

Publications

0 publications found

Variant links:

Genes affected

GOLGA6L22 (HGNC:50289): (golgin A6 family like 22)

GOLGA6L22 links:

ENSG00000310081 (HGNC:):

ENSG00000310081 links:

Genome browser will be placed here

ACMG classification

Classification was made for transcript

Our verdict: Likely_benign. The variant received -2 ACMG points.

BP4

Computational evidence support a benign effect (MetaRNN=0.11809406).

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001396956.1. 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
	GOLGA6L22	NM_001396956.1	MANE Select	c.1396G>A	p.Glu466Lys	missense	Exon 8 of 9	NP_001383885.1	H0YM25
	GOLGA6L22	NM_001396957.1		c.1393G>A	p.Glu465Lys	missense	Exon 8 of 9	NP_001383886.1

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	GOLGA6L22	ENST00000622895.2	TSL:5 MANE Select	c.1396G>A	p.Glu466Lys	missense	Exon 8 of 9	ENSP00000483673.2	H0YM25
	ENSG00000310081	ENST00000846990.1		n.151+4755C>T		intron	N/A

Frequencies

GnomAD3 genomes

AF:

0.00

AC:

AN:

36832

Hom.:

Cov.:

Gnomad AFR

AF:

0.00

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.00

Gnomad ASJ

AF:

0.00

Gnomad EAS

AF:

0.00

Gnomad SAS

AF:

0.00

Gnomad FIN

AF:

0.00

Gnomad MID

AF:

0.00

Gnomad NFE

AF:

0.00

Gnomad OTH

AF:

0.00

GnomAD2 exomes

AF:

0.0000521

AC:

AN:

153556

AF XY:

0.0000369

show subpopulations

Gnomad AFR exome

AF:

0.00

Gnomad AMR exome

AF:

0.00

Gnomad ASJ exome

AF:

0.00

Gnomad EAS exome

AF:

0.000367

Gnomad FIN exome

AF:

0.00

Gnomad NFE exome

AF:

0.0000681

Gnomad OTH exome

AF:

0.00

GnomAD4 exome

AF:

0.0000215

AC:

AN:

792390

Hom.:

Cov.:

AF XY:

0.0000148

AC XY:

AN XY:

405624

show subpopulations

African (AFR)

AF:

0.0000658

AC:

AN:

15202

American (AMR)

AF:

0.000134

AC:

AN:

29786

Ashkenazi Jewish (ASJ)

AF:

0.00

AC:

AN:

16524

East Asian (EAS)

AF:

0.00

AC:

AN:

31108

South Asian (SAS)

AF:

0.0000334

AC:

AN:

59834

European-Finnish (FIN)

AF:

0.00

AC:

AN:

36610

Middle Eastern (MID)

AF:

0.00

AC:

AN:

2182

European-Non Finnish (NFE)

AF:

0.0000176

AC:

AN:

566808

Other (OTH)

AF:

0.00

AC:

AN:

34336

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.438

Heterozygous variant carriers

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Variant carriers

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

GnomAD4 genome

Data not reliable, filtered out with message: AC0

AF:

0.00

AC:

AN:

36832

Hom.:

Cov.:

AF XY:

0.00

AC XY:

AN XY:

17396

African (AFR)

AF:

0.00

AC:

AN:

6154

American (AMR)

AF:

0.00

AC:

AN:

3034

Ashkenazi Jewish (ASJ)

AF:

0.00

AC:

AN:

988

East Asian (EAS)

AF:

0.00

AC:

AN:

1240

South Asian (SAS)

AF:

0.00

AC:

AN:

478

European-Finnish (FIN)

AF:

0.00

AC:

AN:

2404

Middle Eastern (MID)

AF:

0.00

AC:

AN:

European-Non Finnish (NFE)

AF:

0.00

AC:

AN:

21926

Other (OTH)

AF:

0.00

AC:

AN:

394

Alfa

AF:

0.00

Hom.:

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

AlphaMissense

Benign

0.082

BayesDel_addAF

Benign

-0.30

BayesDel_noAF

Benign

-0.67

CADD

Benign

6.9

(source)

DANN

Benign

0.84

Eigen

Benign

-0.44

Eigen_PC

Benign

-0.59

FATHMM_MKL

Benign

0.0032

LIST_S2

Benign

0.52

M_CAP

Benign

0.0078

MetaRNN

Benign

0.12

MetaSVM

Benign

-0.99

PhyloP100

-1.8

PrimateAI

Uncertain

0.59

Sift4G

Benign

0.13

Vest4

0.10

MVP

0.048

ClinPred

0.034

Varity_R

0.051

gMVP

0.019

Mutation Taster

=99/1

polymorphism

(source)

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

You must be logged in to view publications. This limit was set because tens of millions (!) of queries from AI bots are generated daily.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Variant Effect in Transcripts

RefSeq Transcripts

Ensembl Transcripts

Frequencies

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over