chr22-38084652-T-C

Position:

• chr22-38084652-T-C

Variant summary

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

The ENST00000332536.10(BAIAP2L2):​c.*648A>G variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.166 in 152,050 control chromosomes in the GnomAD database, including 2,128 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 0.17 (2128 hom., cov: 33)
• Consequence: BAIAP2L2 ENST00000332536.10 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.573

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]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.188 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
BAIAP2L2	ENST00000332536.10	c.*648A>G		3_prime_UTR_variant	9/9	5
BAIAP2L2	ENST00000681084.1	n.2024A>G		non_coding_transcript_exon_variant	4/4

Frequencies

GnomAD3 genomes AF: 0.166 AC: 25195 AN: 151932 Hom.: 2125 Cov.: 33

Gnomad AFR AF: 0.192

Gnomad AMI AF: 0.208

Gnomad AMR AF: 0.187

Gnomad ASJ AF: 0.133

Gnomad EAS AF: 0.194

Gnomad SAS AF: 0.0864

Gnomad FIN AF: 0.164

Gnomad MID AF: 0.0918

Gnomad NFE AF: 0.151

Gnomad OTH AF: 0.154

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

GnomAD4 genome AF: 0.166 AC: 25222 AN: 152050 Hom.: 2128 Cov.: 33 AF XY: 0.166 AC XY: 12375 AN XY: 74334

Gnomad4 AFR AF: 0.192

Gnomad4 AMR AF: 0.187

Gnomad4 ASJ AF: 0.133

Gnomad4 EAS AF: 0.194

Gnomad4 SAS AF: 0.0871

Gnomad4 FIN AF: 0.164

Gnomad4 NFE AF: 0.151

Gnomad4 OTH AF: 0.155

Alfa AF: 0.152 Hom.: 2347

Bravo AF: 0.167

Asia WGS AF: 0.122 AC: 426 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	1.2
DANN	Benign	0.65

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Other links and lift over

dbSNP: rs2267366; hg19: chr22-38480659;