Variant 22-38087165-G-T details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -11 ACMG points: 0P and 11B. BP4_StrongBP6_ModerateBP7BS2

The NM_025045.6(BAIAP2L2):c.1218C>A(p.Ser406Ser) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00149 in 960,722 control chromosomes in the GnomAD database, including 8 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).

Frequency

Genomes: 𝑓 0.0019 ( 1 hom., cov: 24)

Exomes 𝑓: 0.0014 ( 7 hom. )

Consequence

BAIAP2L2
NM_025045.6 synonymous

Scores

Clinical Significance

Likely benign criteria provided, single submitter B:1

Conservation

PhyloP100: 1.41

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 made for transcript

Verdict is Benign. Variant got -11 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.93).

BP6

Variant 22-38087165-G-T is Benign according to our data. Variant chr22-38087165-G-T is described in ClinVar as [Likely_benign]. Clinvar id is 3234138.Status of the report is criteria_provided_single_submitter, 1 stars.

BP7

Synonymous conserved (PhyloP=1.4 with no splicing effect.

BS2

High Homozygotes in GnomAdExome4 at 7 AR gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
BAIAP2L2	NM_025045.6 link	c.1218C>A	p.Ser406Ser	synonymous_variant	11/14	ENST00000381669.8	NP_079321.3	Q6UXY1-1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
BAIAP2L2	ENST00000381669.8 link	c.1218C>A	p.Ser406Ser	synonymous_variant	11/14	1	NM_025045.6	ENSP00000371085.3		Q6UXY1-1

Frequencies

GnomAD3 genomes

AF:

0.00189

AC:

166

AN:

88026

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.00238

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.00135

Gnomad ASJ

AF:

0.00

Gnomad EAS

AF:

0.00

Gnomad SAS

AF:

0.0117

Gnomad FIN

AF:

0.000525

Gnomad MID

AF:

0.00

Gnomad NFE

AF:

0.00159

Gnomad OTH

AF:

0.000876

GnomAD3 exomes

AF:

0.00167

AC:

372

AN:

222370

Hom.:

AF XY:

0.00195

AC XY:

238

AN XY:

121778

show subpopulations

Gnomad AFR exome

AF:

0.00170

Gnomad AMR exome

AF:

0.00199

Gnomad ASJ exome

AF:

0.000114

Gnomad EAS exome

AF:

0.000613

Gnomad SAS exome

AF:

0.00659

Gnomad FIN exome

AF:

0.000774

Gnomad NFE exome

AF:

0.000786

Gnomad OTH exome

AF:

0.000942

GnomAD4 exome

AF:

0.00145

AC:

1265

AN:

872620

Hom.:

Cov.:

AF XY:

0.00177

AC XY:

783

AN XY:

443272

show subpopulations

Gnomad4 AFR exome

AF:

0.00336

Gnomad4 AMR exome

AF:

0.00286

Gnomad4 ASJ exome

AF:

0.000240

Gnomad4 EAS exome

AF:

0.000280

Gnomad4 SAS exome

AF:

0.00831

Gnomad4 FIN exome

AF:

0.000541

Gnomad4 NFE exome

AF:

0.000784

Gnomad4 OTH exome

AF:

0.00175

GnomAD4 genome

AF:

0.00193

AC:

170

AN:

88102

Hom.:

Cov.:

AF XY:

0.00216

AC XY:

AN XY:

43460

show subpopulations

Gnomad4 AFR

AF:

0.00257

Gnomad4 AMR

AF:

0.00135

Gnomad4 ASJ

AF:

0.00

Gnomad4 EAS

AF:

0.00

Gnomad4 SAS

AF:

0.0113

Gnomad4 FIN

AF:

0.000525

Gnomad4 NFE

AF:

0.00159

Gnomad4 OTH

AF:

0.000868

Alfa

AF:

0.00980

Hom.:

ClinVar

Significance: Likely benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

LINK: link

Submissions by phenotype

not provided

Benign:1

Likely benign, criteria provided, single submitter

clinical testing

CeGaT Center for Human Genetics Tuebingen

Mar 01, 2024

BAIAP2L2: BP4, BP7, BS2 -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.93

CADD

Benign

0.16

DANN

Benign

0.43

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

LitVar

Below is the list of publications found by LitVar. It may be empty.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Submissions by phenotype

Computational scores

Splicing

Publications

LitVar

Other links and lift over