chr22-38093551-G-T

Position:

• chr22-38093551-G-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_025045.6(BAIAP2L2):​c.612+3481C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.381 in 152,074 control chromosomes in the GnomAD database, including 12,575 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 0.38 (12575 hom., cov: 32)
• Consequence: BAIAP2L2 NM_025045.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.38

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 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.543 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
BAIAP2L2	NM_025045.6	c.612+3481C>A		intron_variant		ENST00000381669.8	NP_079321.3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
BAIAP2L2	ENST00000381669.8	c.612+3481C>A		intron_variant		1	NM_025045.6	ENSP00000371085.3

Frequencies

GnomAD3 genomes AF: 0.382 AC: 57984 AN: 151956 Hom.: 12580 Cov.: 32

Gnomad AFR AF: 0.170

Gnomad AMI AF: 0.700

Gnomad AMR AF: 0.484

Gnomad ASJ AF: 0.537

Gnomad EAS AF: 0.405

Gnomad SAS AF: 0.562

Gnomad FIN AF: 0.371

Gnomad MID AF: 0.468

Gnomad NFE AF: 0.460

Gnomad OTH AF: 0.428

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.381 AC: 57987 AN: 152074 Hom.: 12575 Cov.: 32 AF XY: 0.384 AC XY: 28502 AN XY: 74320

Gnomad4 AFR AF: 0.170

Gnomad4 AMR AF: 0.485

Gnomad4 ASJ AF: 0.537

Gnomad4 EAS AF: 0.405

Gnomad4 SAS AF: 0.561

Gnomad4 FIN AF: 0.371

Gnomad4 NFE AF: 0.460

Gnomad4 OTH AF: 0.429

Alfa AF: 0.419 Hom.: 4633

Bravo AF: 0.376

Asia WGS AF: 0.493 AC: 1718 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	6.6
DANN	Benign	0.65

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

Other links and lift over

dbSNP: rs132934; hg19: chr22-38489558;