chr11-96262284-T-A

Variant names:

• chr11-96262284-T-A
• rs11021504
• NM_032427.4:c.513+79099A>T

Variant summary

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

The NM_032427.4(MAML2):​c.513+79099A>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.298 in 152,094 control chromosomes in the GnomAD database, including 8,108 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 0.30 (8108 hom., cov: 32)
• Consequence: MAML2 NM_032427.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.220
• Publications: 10 publications found

Genes affected

MAML2 (HGNC:16259): (mastermind like transcriptional coactivator 2) The protein encoded by this gene is a member of the Mastermind-like family of proteins. All family members are proline and glutamine-rich, and contain a conserved basic domain that binds the ankyrin repeat domain of the intracellular domain of the Notch receptors (ICN1-4) in their N-terminus, and a transcriptional activation domain in their C-terminus. This protein binds to an extended groove that is formed by the interaction of CBF1, Suppressor of Hairless, LAG-1 (CSL) with ICN, and positively regulates Notch signaling. High levels of expression of this gene have been observed in several B cell-derived lymphomas. Translocations resulting in fusion proteins with both CRTC1 and CRTC3 have been implicated in the development of mucoepidermoid carcinomas, while a translocation event with CXCR4 has been linked with chronic lymphocytic leukemia (CLL). Copy number variation in the polyglutamine tract has been observed. [provided by RefSeq, Jan 2015]

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.509 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
MAML2	NM_032427.4	c.513+79099A>T		intron_variant	Intron 1 of 4	ENST00000524717.6	NP_115803.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
MAML2	ENST00000524717.6	c.513+79099A>T		intron_variant	Intron 1 of 4	1	NM_032427.4	ENSP00000434552.1

Frequencies

GnomAD3 genomes AF: 0.298 AC: 45342 AN: 151976 Hom.: 8112 Cov.: 32

Gnomad AFR AF: 0.102

Gnomad AMI AF: 0.309

Gnomad AMR AF: 0.338

Gnomad ASJ AF: 0.330

Gnomad EAS AF: 0.526

Gnomad SAS AF: 0.519

Gnomad FIN AF: 0.434

Gnomad MID AF: 0.247

Gnomad NFE AF: 0.353

Gnomad OTH AF: 0.293

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

GnomAD4 genome AF: 0.298 AC: 45344 AN: 152094 Hom.: 8108 Cov.: 32 AF XY: 0.309 AC XY: 22979 AN XY: 74346

African (AFR) AF: 0.102 AC: 4244 AN: 41520

American (AMR) AF: 0.338 AC: 5170 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.330 AC: 1143 AN: 3466

East Asian (EAS) AF: 0.526 AC: 2721 AN: 5174

South Asian (SAS) AF: 0.517 AC: 2497 AN: 4826

European-Finnish (FIN) AF: 0.434 AC: 4573 AN: 10536

Middle Eastern (MID) AF: 0.238 AC: 70 AN: 294

European-Non Finnish (NFE) AF: 0.353 AC: 24024 AN: 67982

Other (OTH) AF: 0.294 AC: 621 AN: 2110

Alfa AF: 0.193 Hom.: 457

Bravo AF: 0.278

Asia WGS AF: 0.446 AC: 1552 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	1.7
DANN	Benign	0.68
PhyloP100		-0.22
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs11021504; hg19: chr11-95995448;