Genetic Variant ENSG00000296532:n.85+364G>T (chr2-9109909-C-A) – ACMG Classification: Benign (-12 pts)

Variant summary

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

The ENST00000740123.1(ENSG00000296532):n.85+364G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.277 in 152,240 control chromosomes in the GnomAD database, including 6,077 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 0.28 ( 6076 hom., cov: 34)

Exomes 𝑓: 0.23 ( 1 hom. )

Consequence

ENSG00000296532
ENST00000740123.1 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.299

Publications

20 publications found

Variant links:

Genes affected

ENSG00000296532 (HGNC:):

ENSG00000296532 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 (SAS) allele frequency at 95% confidence interval = 0.474 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	Effect
LOC105373414	NR_187857.1 link	n.*50C>A	downstream_gene_variant
LOC105373414	NR_187858.1 link	n.*50C>A	downstream_gene_variant
LOC105373414	NR_187859.1 link	n.*50C>A	downstream_gene_variant

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank	TSL
ENSG00000296532	ENST00000740123.1 link	n.85+364G>T	intron_variant	Intron 1 of 2
ENSG00000296532	ENST00000740127.1 link	n.82+364G>T	intron_variant	Intron 1 of 2
ENSG00000296532	ENST00000740128.1 link	n.83+364G>T	intron_variant	Intron 1 of 2
ENSG00000261104	ENST00000565044.1 link	n.*44C>A	downstream_gene_variant		6

Frequencies

GnomAD3 genomes

AF:

0.277

AC:

42180

AN:

152014

Hom.:

6062

Cov.:

show subpopulations

Gnomad AFR

AF:

0.285

Gnomad AMI

AF:

0.215

Gnomad AMR

AF:

0.335

Gnomad ASJ

AF:

0.276

Gnomad EAS

AF:

0.304

Gnomad SAS

AF:

0.490

Gnomad FIN

AF:

0.237

Gnomad MID

AF:

0.339

Gnomad NFE

AF:

0.249

Gnomad OTH

AF:

0.296

GnomAD4 exome

AF:

0.227

AC:

AN:

110

Hom.:

Cov.:

AF XY:

0.289

AC XY:

AN XY:

show subpopulations

African (AFR)

AC:

AN:

American (AMR)

AC:

AN:

Ashkenazi Jewish (ASJ)

AC:

AN:

East Asian (EAS)

AC:

AN:

South Asian (SAS)

AF:

0.500

AC:

AN:

European-Finnish (FIN)

AF:

0.357

AC:

AN:

Middle Eastern (MID)

AF:

0.00

AC:

AN:

European-Non Finnish (NFE)

AF:

0.200

AC:

AN:

Other (OTH)

AF:

0.250

AC:

AN:

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.495

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:

0.278

AC:

42218

AN:

152130

Hom.:

6076

Cov.:

AF XY:

0.283

AC XY:

21074

AN XY:

74362

show subpopulations

African (AFR)

AF:

0.286

AC:

11854

AN:

41494

American (AMR)

AF:

0.335

AC:

5115

AN:

15282

Ashkenazi Jewish (ASJ)

AF:

0.276

AC:

959

AN:

3472

East Asian (EAS)

AF:

0.305

AC:

1578

AN:

5178

South Asian (SAS)

AF:

0.491

AC:

2367

AN:

4824

European-Finnish (FIN)

AF:

0.237

AC:

2507

AN:

10584

Middle Eastern (MID)

AF:

0.342

AC:

100

AN:

292

European-Non Finnish (NFE)

AF:

0.249

AC:

16925

AN:

67982

Other (OTH)

AF:

0.292

AC:

617

AN:

2110

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.498

Heterozygous variant carriers

1591

3183

4774

6366

7957

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

448

896

1344

1792

2240

<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:

0.265

Hom.:

12013

Bravo

AF:

0.281

Asia WGS

AF:

0.419

AC:

1455

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

1.2

(source)

DANN

Benign

0.71

PhyloP100

0.30

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