dbSNP rs12654778: ENSG00000303969:n.376+881G>A (chr5-148826178-G-A) – ACMG Classification: Benign (-12 pts)

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_ModerateBP6_ModerateBA1

The ENST00000798472.1(ENSG00000303969):n.376+881G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.345 in 155,164 control chromosomes in the GnomAD database, including 9,773 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

Frequency

Genomes: 𝑓 0.34 ( 9503 hom., cov: 31)

Exomes 𝑓: 0.36 ( 270 hom. )

Consequence

ENSG00000303969
ENST00000798472.1 intron

Scores

Clinical Significance

Benign criteria provided, single submitter B:1

Conservation

PhyloP100: 2.60

Publications

45 publications found

Variant links:

Genes affected

ENSG00000303969 (HGNC:):

ENSG00000303969 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=-0.39).

BP6

Variant 5-148826178-G-A is Benign according to our data. Variant chr5-148826178-G-A is described in ClinVar as Benign. ClinVar VariationId is 1180015.Status of the report is criteria_provided_single_submitter, 1 stars.

BA1

GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.379 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
ENSG00000303969	ENST00000798472.1 link	n.376+881G>A		intron_variant	Intron 3 of 4
ENSG00000303969	ENST00000798473.1 link	n.349+881G>A		intron_variant	Intron 3 of 4

Frequencies

GnomAD3 genomes

AF:

0.344

AC:

52246

AN:

151672

Hom.:

9487

Cov.:

show subpopulations

Gnomad AFR

AF:

0.237

Gnomad AMI

AF:

0.207

Gnomad AMR

AF:

0.387

Gnomad ASJ

AF:

0.415

Gnomad EAS

AF:

0.385

Gnomad SAS

AF:

0.388

Gnomad FIN

AF:

0.473

Gnomad MID

AF:

0.367

Gnomad NFE

AF:

0.372

Gnomad OTH

AF:

0.357

GnomAD4 exome

AF:

0.363

AC:

1225

AN:

3374

Hom.:

270

Cov.:

AF XY:

0.357

AC XY:

646

AN XY:

1810

show subpopulations

African (AFR)

AF:

0.0556

AC:

AN:

American (AMR)

AF:

0.324

AC:

AN:

170

Ashkenazi Jewish (ASJ)

AF:

0.353

AC:

AN:

East Asian (EAS)

AF:

0.188

AC:

AN:

South Asian (SAS)

AF:

0.350

AC:

159

AN:

454

European-Finnish (FIN)

AF:

0.422

AC:

146

AN:

346

Middle Eastern (MID)

AF:

0.375

AC:

AN:

European-Non Finnish (NFE)

AF:

0.363

AC:

800

AN:

2204

Other (OTH)

AF:

0.371

AC:

AN:

124

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.514

Heterozygous variant carriers

130

163

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

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:

0.344

AC:

52287

AN:

151790

Hom.:

9503

Cov.:

AF XY:

0.351

AC XY:

26058

AN XY:

74198

show subpopulations

African (AFR)

AF:

0.237

AC:

9798

AN:

41390

American (AMR)

AF:

0.388

AC:

5919

AN:

15270

Ashkenazi Jewish (ASJ)

AF:

0.415

AC:

1438

AN:

3468

East Asian (EAS)

AF:

0.384

AC:

1971

AN:

5128

South Asian (SAS)

AF:

0.390

AC:

1872

AN:

4806

European-Finnish (FIN)

AF:

0.473

AC:

4980

AN:

10536

Middle Eastern (MID)

AF:

0.361

AC:

106

AN:

294

European-Non Finnish (NFE)

AF:

0.372

AC:

25248

AN:

67884

Other (OTH)

AF:

0.364

AC:

766

AN:

2102

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.501

Heterozygous variant carriers

1728

3456

5185

6913

8641

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

526

1052

1578

2104

2630

<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:

0.361

Hom.:

44064

Bravo

AF:

0.332

Asia WGS

AF:

0.399

AC:

1383

AN:

3478

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

LINK: link

Submissions by phenotype

not provided

Benign:1

Jan 09, 2019

GeneDx

Significance:Benign

Review Status:criteria provided, single submitter

Collection Method:clinical testing

This variant is associated with the following publications: (PMID: 29588580) -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.39

CADD

Benign

(source)

DANN

Benign

0.89

PhyloP100

2.6

PromoterAI

-0.11

Neutral

(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

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Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

Age Distribution

Age Distribution

ClinVar

Submissions by phenotype

Computational scores

Splicing

Publications

Other links and lift over