Genetic Variant NM_025045.6:c.1360C>T (chr22-38086349-G-A) – ACMG Classification: Uncertain_significance (0 pts)

Variant summary

Our verdict is Uncertain significance. The variant received 0 ACMG points: 2P and 2B. PM2BP4_Moderate

The NM_025045.6(BAIAP2L2):c.1360C>T(p.Arg454Cys) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000349 in 774,122 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. R454H) has been classified as Uncertain significance.

Frequency

Genomes: 𝑓 0.000045 ( 0 hom., cov: 25)

Exomes 𝑓: 0.000034 ( 0 hom. )

Consequence

BAIAP2L2
NM_025045.6 missense

Scores

Clinical Significance

Uncertain significance criteria provided, single submitter U:1

Conservation

PhyloP100: 1.20

Publications

1 publications found

Variant links:

Genes affected

BAIAP2L2 (HGNC:26203): (BAR/IMD domain containing adaptor protein 2 like 2) The protein encoded by this gene binds phosphoinositides and promotes the formation of planar or curved membrane structures. The encoded protein is found in RAB13-positive vesicles and at intercellular contacts with the plasma membrane. [provided by RefSeq, Dec 2012]

BAIAP2L2 links:

Genome browser will be placed here

ACMG classification

Classification was made for transcript

Our verdict: Uncertain_significance. The variant received 0 ACMG points.

PM2

Very rare variant in population databases, with high coverage;

BP4

Computational evidence support a benign effect (REVEL=0.142).

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_025045.6. 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
	BAIAP2L2	NM_025045.6	MANE Select	c.1360C>T	p.Arg454Cys	missense	Exon 12 of 14	NP_079321.3

Ensembl Transcripts

Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
BAIAP2L2	ENST00000381669.8	TSL:1 MANE Select	c.1360C>T	p.Arg454Cys	missense	Exon 12 of 14	ENSP00000371085.3	Q6UXY1-1
BAIAP2L2	ENST00000871592.1		c.1378C>T	p.Arg460Cys	missense	Exon 12 of 14	ENSP00000541651.1
BAIAP2L2	ENST00000871591.1		c.1360C>T	p.Arg454Cys	missense	Exon 13 of 15	ENSP00000541650.1

Frequencies

GnomAD3 genomes

AF:

0.0000448

AC:

AN:

89356

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0000287

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.00

Gnomad ASJ

AF:

0.00

Gnomad EAS

AF:

0.00

Gnomad SAS

AF:

0.00

Gnomad FIN

AF:

0.00

Gnomad MID

AF:

0.00

Gnomad NFE

AF:

0.0000968

Gnomad OTH

AF:

0.00

GnomAD2 exomes

AF:

0.00000914

AC:

AN:

218894

AF XY:

0.00000837

show subpopulations

Gnomad AFR exome

AF:

0.00

Gnomad AMR exome

AF:

0.00

Gnomad ASJ exome

AF:

0.00

Gnomad EAS exome

AF:

0.00

Gnomad FIN exome

AF:

0.00

Gnomad NFE exome

AF:

0.0000207

Gnomad OTH exome

AF:

0.00

GnomAD4 exome

AF:

0.0000336

AC:

AN:

684766

Hom.:

Cov.:

AF XY:

0.0000177

AC XY:

AN XY:

338346

show subpopulations

African (AFR)

AF:

0.00

AC:

AN:

28266

American (AMR)

AF:

0.00

AC:

AN:

19754

Ashkenazi Jewish (ASJ)

AF:

0.00

AC:

AN:

9994

East Asian (EAS)

AF:

0.00

AC:

AN:

30506

South Asian (SAS)

AF:

0.00

AC:

AN:

37806

European-Finnish (FIN)

AF:

0.00

AC:

AN:

32898

Middle Eastern (MID)

AF:

0.00

AC:

AN:

2624

European-Non Finnish (NFE)

AF:

0.0000445

AC:

AN:

494044

Other (OTH)

AF:

0.0000346

AC:

AN:

28874

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.471

Heterozygous variant carriers

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

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:

0.0000448

AC:

AN:

89356

Hom.:

Cov.:

AF XY:

0.0000228

AC XY:

AN XY:

43922

show subpopulations

African (AFR)

AF:

0.0000287

AC:

AN:

34792

American (AMR)

AF:

0.00

AC:

AN:

7026

Ashkenazi Jewish (ASJ)

AF:

0.00

AC:

AN:

1492

East Asian (EAS)

AF:

0.00

AC:

AN:

4296

South Asian (SAS)

AF:

0.00

AC:

AN:

2200

European-Finnish (FIN)

AF:

0.00

AC:

AN:

7028

Middle Eastern (MID)

AF:

0.00

AC:

AN:

142

European-Non Finnish (NFE)

AF:

0.0000968

AC:

AN:

30982

Other (OTH)

AF:

0.00

AC:

AN:

1070

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.513

Heterozygous variant carriers

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

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

Alfa

AF:

0.0000712

Hom.:

Bravo

AF:

0.0000416

ExAC

AF:

0.0000301

AC:

ClinVar

ClinVar submissions

Significance:Uncertain significance

Revision:criteria provided, single submitter

View on ClinVar

Pathogenic

VUS

Benign

Condition

not specified (1)

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

AlphaMissense

Benign

0.092

BayesDel_addAF

Pathogenic

0.21

BayesDel_noAF

Benign

-0.25

CADD

Uncertain

(source)

DANN

Uncertain

1.0

Eigen

Benign

0.025

Eigen_PC

Benign

-0.062

FATHMM_MKL

Benign

0.057

M_CAP

Benign

0.027

PhyloP100

1.2

ClinPred

0.70

GERP RS

1.9

Varity_R

0.081

Mutation Taster

=93/7

polymorphism

(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

You must be logged in to view publications. This limit was set because tens of millions (!) of queries from AI bots are generated daily.

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