Genetic Variant NM_019043.4:c.72+61G>A (chr10-26492459-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_019043.4(APBB1IP):c.72+61G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.769 in 1,480,308 control chromosomes in the GnomAD database, including 439,933 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 0.80 ( 49552 hom., cov: 32)

Exomes 𝑓: 0.76 ( 390381 hom. )

Consequence

APBB1IP
NM_019043.4 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.159

Publications

8 publications found

Variant links:

Genes affected

APBB1IP (HGNC:17379): (amyloid beta precursor protein binding family B member 1 interacting protein) Predicted to be involved in signal transduction. Predicted to act upstream of or within T cell activation via T cell receptor contact with antigen bound to MHC molecule on antigen presenting cell and positive regulation of cell adhesion. Located in cytosol and plasma membrane. [provided by Alliance of Genome Resources, Apr 2022]

APBB1IP 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=-0.87).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.878 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_019043.4. 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
	APBB1IP	NM_019043.4	MANE Select	c.72+61G>A		intron	N/A	NP_061916.3

Ensembl Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein	UniProt
APBB1IP	ENST00000376236.9	TSL:5 MANE Select	c.72+61G>A	intron	N/A	ENSP00000365411.4	Q7Z5R6-1
APBB1IP	ENST00000356785.4	TSL:1	c.72+61G>A	intron	N/A	ENSP00000349237.4	Q7Z5R6-2
APBB1IP	ENST00000718302.1		c.72+61G>A	intron	N/A	ENSP00000520735.1	Q7Z5R6-1

Frequencies

GnomAD3 genomes

AF:

0.804

AC:

122209

AN:

152090

Hom.:

49490

Cov.:

show subpopulations

Gnomad AFR

AF:

0.886

Gnomad AMI

AF:

0.789

Gnomad AMR

AF:

0.785

Gnomad ASJ

AF:

0.815

Gnomad EAS

AF:

0.888

Gnomad SAS

AF:

0.828

Gnomad FIN

AF:

0.835

Gnomad MID

AF:

0.772

Gnomad NFE

AF:

0.745

Gnomad OTH

AF:

0.784

GnomAD4 exome

AF:

0.765

AC:

1015706

AN:

1328100

Hom.:

390381

AF XY:

0.766

AC XY:

511476

AN XY:

667890

show subpopulations

African (AFR)

AF:

0.888

AC:

26945

AN:

30332

American (AMR)

AF:

0.847

AC:

36554

AN:

43154

Ashkenazi Jewish (ASJ)

AF:

0.807

AC:

20280

AN:

25140

East Asian (EAS)

AF:

0.911

AC:

35463

AN:

38940

South Asian (SAS)

AF:

0.821

AC:

67902

AN:

82690

European-Finnish (FIN)

AF:

0.823

AC:

43538

AN:

52902

Middle Eastern (MID)

AF:

0.785

AC:

4278

AN:

5448

European-Non Finnish (NFE)

AF:

0.742

AC:

737596

AN:

993796

Other (OTH)

AF:

0.775

AC:

43150

AN:

55698

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.497

Heterozygous variant carriers

11066

22133

33199

44266

55332

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

17346

34692

52038

69384

86730

<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:

0.804

AC:

122328

AN:

152208

Hom.:

49552

Cov.:

AF XY:

0.808

AC XY:

60148

AN XY:

74400

show subpopulations

African (AFR)

AF:

0.886

AC:

36798

AN:

41530

American (AMR)

AF:

0.785

AC:

12015

AN:

15306

Ashkenazi Jewish (ASJ)

AF:

0.815

AC:

2831

AN:

3472

East Asian (EAS)

AF:

0.888

AC:

4592

AN:

5170

South Asian (SAS)

AF:

0.827

AC:

3988

AN:

4824

European-Finnish (FIN)

AF:

0.835

AC:

8857

AN:

10604

Middle Eastern (MID)

AF:

0.769

AC:

226

AN:

294

European-Non Finnish (NFE)

AF:

0.745

AC:

50638

AN:

67982

Other (OTH)

AF:

0.787

AC:

1663

AN:

2114

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.501

Heterozygous variant carriers

1215

2430

3646

4861

6076

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

874

1748

2622

3496

4370

<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:

0.767

Hom.:

15354

Bravo

AF:

0.806

Asia WGS

AF:

0.853

AC:

2964

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.87

CADD

Benign

2.9

(source)

DANN

Benign

0.67

PhyloP100

-0.16

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