11-95977868-G-T

Position:

• chr11-95977868-G-T

Variant summary

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

The NM_032427.4(MAML2):​c.*1080C>A variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.219 in 225,130 control chromosomes in the GnomAD database, including 6,047 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 0.24 (4766 hom., cov: 33)
  • Exomes 𝑓: 0.18 (1281 hom.)
• Consequence: MAML2 NM_032427.4 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0590

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

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.318 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
MAML2	NM_032427.4	c.*1080C>A		3_prime_UTR_variant	5/5	ENST00000524717.6	NP_115803.1
MAML2	XM_011543023.4	c.*1080C>A		3_prime_UTR_variant	5/5		XP_011541325.1
MAML2	XM_047427710.1	c.*1080C>A		3_prime_UTR_variant	5/5		XP_047283666.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
MAML2	ENST00000524717.6	c.*1080C>A		3_prime_UTR_variant	5/5	1	NM_032427.4	ENSP00000434552	P1

Frequencies

GnomAD3 genomes AF: 0.237 AC: 35963 AN: 151904 Hom.: 4751 Cov.: 33

Gnomad AFR AF: 0.308

Gnomad AMI AF: 0.316

Gnomad AMR AF: 0.325

Gnomad ASJ AF: 0.133

Gnomad EAS AF: 0.131

Gnomad SAS AF: 0.223

Gnomad FIN AF: 0.282

Gnomad MID AF: 0.259

Gnomad NFE AF: 0.180

Gnomad OTH AF: 0.229

GnomAD4 exome AF: 0.181 AC: 13250 AN: 73108 Hom.: 1281 Cov.: 0 AF XY: 0.179 AC XY: 6037 AN XY: 33736

Gnomad4 AFR exome AF: 0.310

Gnomad4 AMR exome AF: 0.324

Gnomad4 ASJ exome AF: 0.148

Gnomad4 EAS exome AF: 0.118

Gnomad4 SAS exome AF: 0.200

Gnomad4 FIN exome AF: 0.190

Gnomad4 NFE exome AF: 0.180

Gnomad4 OTH exome AF: 0.195

GnomAD4 genome AF: 0.237 AC: 36026 AN: 152022 Hom.: 4766 Cov.: 33 AF XY: 0.243 AC XY: 18088 AN XY: 74312

Gnomad4 AFR AF: 0.308

Gnomad4 AMR AF: 0.325

Gnomad4 ASJ AF: 0.133

Gnomad4 EAS AF: 0.132

Gnomad4 SAS AF: 0.223

Gnomad4 FIN AF: 0.282

Gnomad4 NFE AF: 0.180

Gnomad4 OTH AF: 0.229

Alfa AF: 0.176 Hom.: 1267

Bravo AF: 0.244

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	1.2
DANN	Benign	0.68

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: rs7114756; hg19: chr11-95711032;