dbSNP rs6838908: BOD1L1:c.8353+111T>C (chr4-13587588-A-G) – ACMG Classification: Benign (-12 pts)

Variant summary

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

The NM_148894.3(BOD1L1):c.8353+111T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.795 in 765,992 control chromosomes in the GnomAD database, including 248,364 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 0.70 ( 40956 hom., cov: 31)

Exomes 𝑓: 0.82 ( 207408 hom. )

Consequence

BOD1L1
NM_148894.3 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.697

Publications

4 publications found

Variant links:

Genes affected

BOD1L1 (HGNC:31792): (biorientation of chromosomes in cell division 1 like 1) Predicted to enable protein phosphatase 2A binding activity and protein phosphatase inhibitor activity. Involved in cellular response to DNA damage stimulus and replication fork processing. Located in nucleoplasm. [provided by Alliance of Genome Resources, Apr 2022]

BOD1L1 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=-0.88).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.938 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_148894.3. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	BOD1L1	NM_148894.3	MANE Select	c.8353+111T>C		intron	N/A	NP_683692.2	Q8NFC6

Ensembl Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein	UniProt
BOD1L1	ENST00000040738.10	TSL:1 MANE Select	c.8353+111T>C	intron	N/A	ENSP00000040738.5	Q8NFC6
BOD1L1	ENST00000927662.1		c.8353+111T>C	intron	N/A	ENSP00000597721.1
BOD1L1	ENST00000507943.2	TSL:3	c.8353+111T>C	intron	N/A	ENSP00000425492.2	H0Y9Y2

Frequencies

GnomAD3 genomes

AF:

0.703

AC:

106766

AN:

151974

Hom.:

40934

Cov.:

show subpopulations

Gnomad AFR

AF:

0.371

Gnomad AMI

AF:

0.914

Gnomad AMR

AF:

0.826

Gnomad ASJ

AF:

0.806

Gnomad EAS

AF:

0.960

Gnomad SAS

AF:

0.872

Gnomad FIN

AF:

0.848

Gnomad MID

AF:

0.766

Gnomad NFE

AF:

0.813

Gnomad OTH

AF:

0.720

GnomAD4 exome

AF:

0.818

AC:

501867

AN:

613900

Hom.:

207408

AF XY:

0.821

AC XY:

263839

AN XY:

321504

show subpopulations

African (AFR)

AF:

0.365

AC:

5625

AN:

15408

American (AMR)

AF:

0.870

AC:

20649

AN:

23726

Ashkenazi Jewish (ASJ)

AF:

0.819

AC:

12799

AN:

15624

East Asian (EAS)

AF:

0.960

AC:

29861

AN:

31106

South Asian (SAS)

AF:

0.867

AC:

42503

AN:

49018

European-Finnish (FIN)

AF:

0.851

AC:

37203

AN:

43730

Middle Eastern (MID)

AF:

0.766

AC:

1743

AN:

2276

European-Non Finnish (NFE)

AF:

0.813

AC:

327155

AN:

402554

Other (OTH)

AF:

0.799

AC:

24329

AN:

30458

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.499

Heterozygous variant carriers

4119

8238

12358

16477

20596

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

4136

8272

12408

16544

20680

<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:

0.702

AC:

106817

AN:

152092

Hom.:

40956

Cov.:

AF XY:

0.710

AC XY:

52833

AN XY:

74384

show subpopulations

African (AFR)

AF:

0.370

AC:

15349

AN:

41440

American (AMR)

AF:

0.826

AC:

12626

AN:

15282

Ashkenazi Jewish (ASJ)

AF:

0.806

AC:

2797

AN:

3470

East Asian (EAS)

AF:

0.960

AC:

4965

AN:

5170

South Asian (SAS)

AF:

0.873

AC:

4213

AN:

4824

European-Finnish (FIN)

AF:

0.848

AC:

8995

AN:

10602

Middle Eastern (MID)

AF:

0.762

AC:

224

AN:

294

European-Non Finnish (NFE)

AF:

0.813

AC:

55286

AN:

67986

Other (OTH)

AF:

0.723

AC:

1528

AN:

2112

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.503

Heterozygous variant carriers

1297

2595

3892

5190

6487

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

802

1604

2406

3208

4010

<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:

0.729

Hom.:

5570

Bravo

AF:

0.687

Asia WGS

AF:

0.880

AC:

3059

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.88

CADD

Benign

2.0

(source)

DANN

Benign

0.77

PhyloP100

-0.70

Mutation Taster

=100/0

polymorphism (auto)

(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

Variant Effect in Transcripts

RefSeq Transcripts

Ensembl Transcripts

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over