rs2267366

Variant names:

• chr22-38084652-T-C
• rs2267366
• ENST00000332536.10:c.*648A>G

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000681084.1(BAIAP2L2):​n.2024A>G variant causes a splice region, non coding transcript exon 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 ENST00000681084.1 splice_region, non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.573
• Publications: 13 publications found

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

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000681084.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	BAIAP2L2	NM_025045.6	MANE Select	c.*648A>G		downstream_gene	N/A	NP_079321.3

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	BAIAP2L2	ENST00000332536.10	TSL:5	c.*648A>G		splice_region	Exon 9 of 9	ENSP00000328876.7
	BAIAP2L2	ENST00000332536.10	TSL:5	c.*648A>G		3_prime_UTR	Exon 9 of 9	ENSP00000328876.7
	BAIAP2L2	ENST00000681084.1		n.2024A>G		splice_region non_coding_transcript_exon	Exon 4 of 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

African (AFR) AF: 0.192 AC: 7950 AN: 41476

American (AMR) AF: 0.187 AC: 2865 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.133 AC: 461 AN: 3466

East Asian (EAS) AF: 0.194 AC: 1004 AN: 5168

South Asian (SAS) AF: 0.0871 AC: 421 AN: 4832

European-Finnish (FIN) AF: 0.164 AC: 1736 AN: 10588

Middle Eastern (MID) AF: 0.0918 AC: 27 AN: 294

European-Non Finnish (NFE) AF: 0.151 AC: 10243 AN: 67920

Other (OTH) AF: 0.155 AC: 326 AN: 2108

Alfa AF: 0.153 Hom.: 3018

Bravo AF: 0.167

Asia WGS AF: 0.122 AC: 426 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	1.2
DANN	Benign	0.65
PhyloP100		-0.57
PromoterAI		0.025	Neutral

Splicing

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

Other links and lift over

dbSNP: rs2267366; hg19: chr22-38480659;