Genetic Variant LOC285819:n.237G>A (chr6-26478922-C-T) – ACMG Classification: Benign (-12 pts)

Variant summary

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

The NR_038992.1(LOC285819):n.237G>A 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 0.108 in 151,952 control chromosomes in the GnomAD database, including 943 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 0.11 ( 943 hom., cov: 32)

Consequence

LOC285819
NR_038992.1 non_coding_transcript_exon

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -1.47

Publications

28 publications found

Variant links:

Genes affected

LOC285819 (HGNC:):

LOC285819 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=-0.91).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.132 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC285819	NR_038992.1 link	n.237G>A		non_coding_transcript_exon_variant	Exon 2 of 4

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank
ENSG00000291336	ENST00000707189.1 link	n.1000-74265C>T	intron_variant	Intron 1 of 1
ENSG00000291338	ENST00000707191.1 link	n.1001-53783C>T	intron_variant	Intron 1 of 1
ENSG00000300236	ENST00000770281.1 link	n.559-6729G>A	intron_variant	Intron 5 of 5

Frequencies

GnomAD3 genomes

AF:

0.108

AC:

16408

AN:

151836

Hom.:

943

Cov.:

show subpopulations

Gnomad AFR

AF:

0.135

Gnomad AMI

AF:

0.207

Gnomad AMR

AF:

0.0516

Gnomad ASJ

AF:

0.0384

Gnomad EAS

AF:

0.0987

Gnomad SAS

AF:

0.117

Gnomad FIN

AF:

0.0776

Gnomad MID

AF:

0.0665

Gnomad NFE

AF:

0.112

Gnomad OTH

AF:

0.0876

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome

AF:

0.108

AC:

16418

AN:

151952

Hom.:

943

Cov.:

AF XY:

0.104

AC XY:

7743

AN XY:

74276

show subpopulations

African (AFR)

AF:

0.135

AC:

5580

AN:

41408

American (AMR)

AF:

0.0514

AC:

786

AN:

15278

Ashkenazi Jewish (ASJ)

AF:

0.0384

AC:

133

AN:

3466

East Asian (EAS)

AF:

0.0989

AC:

512

AN:

5176

South Asian (SAS)

AF:

0.117

AC:

560

AN:

4806

European-Finnish (FIN)

AF:

0.0776

AC:

819

AN:

10548

Middle Eastern (MID)

AF:

0.0612

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.112

AC:

7637

AN:

67956

Other (OTH)

AF:

0.0877

AC:

185

AN:

2110

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.501

Heterozygous variant carriers

733

1466

2200

2933

3666

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

192

384

576

768

960

<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:

0.110

Hom.:

3165

Bravo

AF:

0.106

Asia WGS

AF:

0.106

AC:

368

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.91

CADD

Benign

0.10

(source)

DANN

Benign

0.27

PhyloP100

-1.5

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

ClinVar

Computational scores

Splicing

Publications

Other links and lift over