Genetic Variant NEUROG2-AS1:n.549C>G (chr4-112518056-C-G) – ACMG Classification: Benign (-12 pts)

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBA1

The ENST00000506057.2(NEUROG2-AS1):n.549C>G variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.47 in 151,968 control chromosomes in the GnomAD database, including 16,961 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: 𝑓 0.47 ( 16961 hom., cov: 32)

Exomes 𝑓: 0.50 ( 0 hom. )

Consequence

NEUROG2-AS1
ENST00000506057.2 non_coding_transcript_exon

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.893

Publications

4 publications found

Variant links:

Genes affected

NEUROG2-AS1 (HGNC:40656): (NEUROG2 and ZGRF1 antisense RNA 1)

NEUROG2-AS1 links:

LOC124900760 (HGNC:):

LOC124900760 links:

Genome browser will be placed here

ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -12 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.84).

BA1

GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.522 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC124900760	XR_007058231.1 link	n.484C>G		non_coding_transcript_exon_variant	Exon 2 of 2
NEUROG2-AS1	NR_161159.1 link	n.262+2416C>G		intron_variant	Intron 1 of 3

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank	TSL
NEUROG2-AS1	ENST00000506057.2 link	n.549C>G	non_coding_transcript_exon_variant	Exon 2 of 2	3
NEUROG2-AS1	ENST00000754798.1 link	n.502C>G	non_coding_transcript_exon_variant	Exon 2 of 2
NEUROG2-AS1	ENST00000754799.1 link	n.647C>G	non_coding_transcript_exon_variant	Exon 3 of 3

Frequencies

GnomAD3 genomes

AF:

0.470

AC:

71415

AN:

151848

Hom.:

16953

Cov.:

show subpopulations

Gnomad AFR

AF:

0.445

Gnomad AMI

AF:

0.346

Gnomad AMR

AF:

0.531

Gnomad ASJ

AF:

0.420

Gnomad EAS

AF:

0.336

Gnomad SAS

AF:

0.469

Gnomad FIN

AF:

0.525

Gnomad MID

AF:

0.415

Gnomad NFE

AF:

0.479

Gnomad OTH

AF:

0.448

GnomAD4 exome

AF:

0.500

AC:

AN:

Hom.:

Cov.:

AC XY:

AN XY:

show subpopulations

African (AFR)

AC:

AN:

American (AMR)

AC:

AN:

Ashkenazi Jewish (ASJ)

AC:

AN:

East Asian (EAS)

AF:

0.500

AC:

AN:

South Asian (SAS)

AC:

AN:

European-Finnish (FIN)

AC:

AN:

Middle Eastern (MID)

AC:

AN:

European-Non Finnish (NFE)

AC:

AN:

Other (OTH)

AC:

AN:

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.675

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

AF:

0.470

AC:

71457

AN:

151966

Hom.:

16961

Cov.:

AF XY:

0.471

AC XY:

35002

AN XY:

74264

show subpopulations

African (AFR)

AF:

0.445

AC:

18408

AN:

41394

American (AMR)

AF:

0.532

AC:

8122

AN:

15276

Ashkenazi Jewish (ASJ)

AF:

0.420

AC:

1456

AN:

3468

East Asian (EAS)

AF:

0.336

AC:

1739

AN:

5174

South Asian (SAS)

AF:

0.471

AC:

2271

AN:

4824

European-Finnish (FIN)

AF:

0.525

AC:

5533

AN:

10542

Middle Eastern (MID)

AF:

0.408

AC:

120

AN:

294

European-Non Finnish (NFE)

AF:

0.479

AC:

32547

AN:

67968

Other (OTH)

AF:

0.447

AC:

945

AN:

2114

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.501

Heterozygous variant carriers

1927

3854

5780

7707

9634

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

650

1300

1950

2600

3250

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

Alfa

AF:

0.305

Hom.:

703

Bravo

AF:

0.468

Asia WGS

AF:

0.480

AC:

1665

AN:

3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.84

CADD

Benign

1.1

(source)

DANN

Benign

0.39

PhyloP100

-0.89

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

Transcripts

RefSeq

Ensembl

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over