Genetic Variant ENSG00000305927:n.90+962C>G (chr2-96747751-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 ENST00000814154.1(ENSG00000305927):n.90+962C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.268 in 152,008 control chromosomes in the GnomAD database, including 6,052 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 0.27 ( 6052 hom., cov: 32)

Consequence

ENSG00000305927
ENST00000814154.1 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.635

Publications

28 publications found

Variant links:

Genes affected

ENSG00000305927 (HGNC:):

ENSG00000305927 links:

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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=-0.8).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.309 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000305927	ENST00000814154.1 link	n.90+962C>G		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes

AF:

0.269

AC:

40787

AN:

151888

Hom.:

6058

Cov.:

show subpopulations

Gnomad AFR

AF:

0.187

Gnomad AMI

AF:

0.208

Gnomad AMR

AF:

0.200

Gnomad ASJ

AF:

0.214

Gnomad EAS

AF:

0.322

Gnomad SAS

AF:

0.184

Gnomad FIN

AF:

0.447

Gnomad MID

AF:

0.237

Gnomad NFE

AF:

0.313

Gnomad OTH

AF:

0.223

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

GnomAD4 genome

AF:

0.268

AC:

40793

AN:

152008

Hom.:

6052

Cov.:

AF XY:

0.272

AC XY:

20174

AN XY:

74304

show subpopulations

African (AFR)

AF:

0.187

AC:

7754

AN:

41476

American (AMR)

AF:

0.200

AC:

3053

AN:

15266

Ashkenazi Jewish (ASJ)

AF:

0.214

AC:

743

AN:

3468

East Asian (EAS)

AF:

0.321

AC:

1658

AN:

5166

South Asian (SAS)

AF:

0.184

AC:

886

AN:

4824

European-Finnish (FIN)

AF:

0.447

AC:

4707

AN:

10536

Middle Eastern (MID)

AF:

0.241

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.313

AC:

21266

AN:

67950

Other (OTH)

AF:

0.220

AC:

465

AN:

2116

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.499

Heterozygous variant carriers

1479

2958

4436

5915

7394

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

418

836

1254

1672

2090

<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:

0.297

Hom.:

3922

Bravo

AF:

0.250

Asia WGS

AF:

0.261

AC:

911

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.80

CADD

Benign

3.8

(source)

DANN

Benign

0.51

PhyloP100

0.64

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