Variant 4-13582305-A-G details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong

The NM_148894.3(BOD1L1):c.8524T>C(p.Tyr2842His) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000137 in 1,460,468 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 15/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).

Frequency

Genomes: not found (cov: 32)

Exomes 𝑓: 0.0000014 ( 0 hom. )

Consequence

BOD1L1
NM_148894.3 missense

Scores

Clinical Significance

Uncertain significance criteria provided, single submitter U:1

Conservation

PhyloP100: 0.264

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:

BOD1L1 (HGNC:):

BOD1L1 links:

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ACMG classification

Classification made for transcript

Verdict is Likely_benign. Variant got -2 ACMG points.

PM2

Very rare variant in population databases, with high coverage;

BP4

Computational evidence support a benign effect (MetaRNN=0.031998366).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
BOD1L1	NM_148894.3 linkuse as main transcript	c.8524T>C	p.Tyr2842His	missense_variant	19/26	ENST00000040738.10	NP_683692.2	Q8NFC6

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	UniProt
BOD1L1	ENST00000040738.10 linkuse as main transcript	c.8524T>C	p.Tyr2842His	missense_variant	19/26	1	NM_148894.3	ENSP00000040738.5	Q8NFC6
BOD1L1	ENST00000507943.2 linkuse as main transcript	c.8524T>C	p.Tyr2842His	missense_variant	19/27	3		ENSP00000425492.2	H0Y9Y2
BOD1L1	ENST00000511119.1 linkuse as main transcript	n.1974T>C		non_coding_transcript_exon_variant	7/7	4

Frequencies

GnomAD3 genomes

Cov.:

GnomAD4 exome

AF:

0.00000137

AC:

AN:

1460468

Hom.:

Cov.:

AF XY:

0.00000138

AC XY:

AN XY:

726570

show subpopulations

Gnomad4 AFR exome

AF:

0.00

Gnomad4 AMR exome

AF:

0.00

Gnomad4 ASJ exome

AF:

0.00

Gnomad4 EAS exome

AF:

0.00

Gnomad4 SAS exome

AF:

0.00

Gnomad4 FIN exome

AF:

0.00

Gnomad4 NFE exome

AF:

0.00000180

Gnomad4 OTH exome

AF:

0.00

GnomAD4 genome

Cov.:

ClinVar

Significance: Uncertain significance

Submissions summary: Uncertain:1

Revision: criteria provided, single submitter

LINK: link

Submissions by phenotype

not specified

Uncertain:1

Uncertain significance, criteria provided, single submitter

clinical testing

Ambry Genetics

Nov 08, 2022

The c.8524T>C (p.Y2842H) alteration is located in exon 19 (coding exon 19) of the BOD1L1 gene. This alteration results from a T to C substitution at nucleotide position 8524, causing the tyrosine (Y) at amino acid position 2842 to be replaced by a histidine (H). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

AlphaMissense

Benign

0.20

BayesDel_addAF

Benign

-0.26

BayesDel_noAF

Benign

-0.62

CADD

Benign

7.4

DANN

Benign

0.96

DEOGEN2

Benign

0.020

Eigen

Benign

-1.1

Eigen_PC

Benign

-1.1

FATHMM_MKL

Benign

0.037

LIST_S2

Benign

0.73

M_CAP

Benign

0.0096

MetaRNN

Benign

0.032

MetaSVM

Benign

-0.96

MutationAssessor

Benign

1.6

PrimateAI

Benign

0.29

PROVEAN

Benign

-1.1

REVEL

Benign

0.034

Sift

Pathogenic

0.0

Sift4G

Benign

0.46

Polyphen

0.031

Vest4

0.34

MutPred

0.16

Loss of phosphorylation at Y2842 (P = 7e-04);

MVP

0.11

MPC

0.22

ClinPred

0.50

GERP RS

-3.0

Varity_R

0.16

gMVP

0.042

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

No publications associated with this variant yet.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Submissions by phenotype

Computational scores

Splicing

Publications

Other links and lift over