dbSNP rs181405: BID:c.-58-60C>T (chr22-17750234-G-A) – ACMG Classification: Benign (-12 pts)

Variant summary

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

The NM_001196.4(BID):c.-58-60C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.461 in 1,461,104 control chromosomes in the GnomAD database, including 162,393 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 0.39 ( 13764 hom., cov: 34)

Exomes 𝑓: 0.47 ( 148629 hom. )

Consequence

BID
NM_001196.4 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.702

Publications

12 publications found

Variant links:

Genes affected

BID (HGNC:1050): (BH3 interacting domain death agonist) This gene encodes a death agonist that heterodimerizes with either agonist BAX or antagonist BCL2, and thus regulate apoptosis. The encoded protein is a member of the BCL-2 family of cell death regulators. It is a mediator of mitochondrial damage induced by caspase-8 (CASP8); CASP8 cleaves this encoded protein, and the COOH-terminal part translocates to mitochondria where it triggers cytochrome c release. Multiple alternatively spliced transcript variants have been found. [provided by RefSeq, Aug 2020]

BID 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 (EAS) allele frequency at 95% confidence interval = 0.733 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
BID	NM_001196.4 link	c.-58-60C>T		intron_variant	Intron 1 of 5	ENST00000622694.5	NP_001187.1	P55957-1A8ASI8B3KT21

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
BID	ENST00000622694.5 link	c.-58-60C>T		intron_variant	Intron 1 of 5	1	NM_001196.4	ENSP00000480414.1		P55957-1

Frequencies

GnomAD3 genomes

AF:

0.393

AC:

59798

AN:

152122

Hom.:

13755

Cov.:

show subpopulations

Gnomad AFR

AF:

0.164

Gnomad AMI

AF:

0.569

Gnomad AMR

AF:

0.527

Gnomad ASJ

AF:

0.484

Gnomad EAS

AF:

0.753

Gnomad SAS

AF:

0.596

Gnomad FIN

AF:

0.403

Gnomad MID

AF:

0.446

Gnomad NFE

AF:

0.451

Gnomad OTH

AF:

0.434

GnomAD4 exome

AF:

0.469

AC:

614260

AN:

1308864

Hom.:

148629

AF XY:

0.473

AC XY:

308711

AN XY:

652644

show subpopulations

African (AFR)

AF:

0.149

AC:

4483

AN:

30134

American (AMR)

AF:

0.606

AC:

22585

AN:

37298

Ashkenazi Jewish (ASJ)

AF:

0.487

AC:

11994

AN:

24610

East Asian (EAS)

AF:

0.749

AC:

27204

AN:

36298

South Asian (SAS)

AF:

0.582

AC:

45659

AN:

78484

European-Finnish (FIN)

AF:

0.402

AC:

19631

AN:

48890

Middle Eastern (MID)

AF:

0.491

AC:

2682

AN:

5466

European-Non Finnish (NFE)

AF:

0.457

AC:

454052

AN:

992612

Other (OTH)

AF:

0.472

AC:

25970

AN:

55072

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.499

Heterozygous variant carriers

15604

31208

46813

62417

78021

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

13356

26712

40068

53424

66780

<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:

0.393

AC:

59826

AN:

152240

Hom.:

13764

Cov.:

AF XY:

0.399

AC XY:

29680

AN XY:

74422

show subpopulations

African (AFR)

AF:

0.164

AC:

6817

AN:

41558

American (AMR)

AF:

0.528

AC:

8073

AN:

15298

Ashkenazi Jewish (ASJ)

AF:

0.484

AC:

1680

AN:

3472

East Asian (EAS)

AF:

0.752

AC:

3885

AN:

5164

South Asian (SAS)

AF:

0.596

AC:

2877

AN:

4830

European-Finnish (FIN)

AF:

0.403

AC:

4279

AN:

10608

Middle Eastern (MID)

AF:

0.442

AC:

130

AN:

294

European-Non Finnish (NFE)

AF:

0.451

AC:

30639

AN:

67994

Other (OTH)

AF:

0.439

AC:

929

AN:

2114

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.500

Heterozygous variant carriers

1773

3545

5318

7090

8863

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

564

1128

1692

2256

2820

<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:

0.431

Hom.:

11656

Bravo

AF:

0.394

Asia WGS

AF:

0.635

AC:

2204

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

2.9

(source)

DANN

Benign

0.59

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

Transcripts

RefSeq

Ensembl

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over