9-21815590-T-TAA

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP6_Moderate BA1

The NM_002451.4(MTAP):c.120+84_120+85dup variant causes a intron change involving the alteration of a non-conserved nucleotide. Variant has been reported in ClinVar as Benign (★).

• Frequency:
  • Genomes: 𝑓 0.18 (2885 hom., cov: 0)
  • Exomes 𝑓: 0.36 (454 hom.)
• Consequence: MTAP NM_002451.4 intron
• Clinical Significance: Benign criteria provided, single submitter B:1
• Conservation: PhyloP100: 0.529

Genes affected

MTAP (HGNC:7413): (methylthioadenosine phosphorylase) This gene encodes an enzyme that plays a major role in polyamine metabolism and is important for the salvage pathway of both adenine and methionine. The encoded enzyme is deficient in many cancers. Multiple alternatively spliced transcript variants have been described for this gene. [provided by RefSeq, Sep 2021]

ACMG classification

Verdict is Benign. Variant got -10 ACMG points.

• BP6: Variant 9-21815590-T-TAA is Benign according to our data. Variant chr9-21815590-T-TAA is described in ClinVar as [Benign]. Clinvar id is 1276709.Status of the report is criteria_provided_single_submitter, 1 stars.
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.294 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
MTAP	NM_002451.4	c.120+84_120+85dup		intron_variant		ENST00000644715.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
MTAP	ENST00000644715.2	c.120+84_120+85dup		intron_variant			NM_002451.4	P1

Frequencies

GnomAD3 genomes AF: 0.183 AC: 26637 AN: 145926 Hom.: 2881 Cov.: 0

Gnomad AFR AF: 0.298

Gnomad AMI AF: 0.330

Gnomad AMR AF: 0.183

Gnomad ASJ AF: 0.162

Gnomad EAS AF: 0.273

Gnomad SAS AF: 0.164

Gnomad FIN AF: 0.148

Gnomad MID AF: 0.218

Gnomad NFE AF: 0.112

Gnomad OTH AF: 0.172

GnomAD3 exomes AF: 0.414 AC: 35446 AN: 85622 Hom.: 285 AF XY: 0.413 AC XY: 19306 AN XY: 46708

Gnomad AFR exome AF: 0.421

Gnomad AMR exome AF: 0.398

Gnomad ASJ exome AF: 0.412

Gnomad EAS exome AF: 0.419

Gnomad SAS exome AF: 0.416

Gnomad FIN exome AF: 0.456

Gnomad NFE exome AF: 0.402

Gnomad OTH exome AF: 0.404

GnomAD4 exome AF: 0.364 AC: 212659 AN: 584196 Hom.: 454 Cov.: 12 AF XY: 0.368 AC XY: 114337 AN XY: 310646

Gnomad4 AFR exome AF: 0.382

Gnomad4 AMR exome AF: 0.376

Gnomad4 ASJ exome AF: 0.374

Gnomad4 EAS exome AF: 0.394

Gnomad4 SAS exome AF: 0.400

Gnomad4 FIN exome AF: 0.403

Gnomad4 NFE exome AF: 0.351

Gnomad4 OTH exome AF: 0.368

GnomAD4 genome AF: 0.183 AC: 26662 AN: 145980 Hom.: 2885 Cov.: 0 AF XY: 0.184 AC XY: 13022 AN XY: 70670

Gnomad4 AFR AF: 0.299

Gnomad4 AMR AF: 0.183

Gnomad4 ASJ AF: 0.162

Gnomad4 EAS AF: 0.273

Gnomad4 SAS AF: 0.164

Gnomad4 FIN AF: 0.148

Gnomad4 NFE AF: 0.112

Gnomad4 OTH AF: 0.171

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

Submissions by phenotype

not provided Benign:1

Benign, criteria provided, single submitter

clinical testing

GeneDx

Jun 20, 2021

- -

Computational scores

Source: dbNSFP v4.3

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4007652; hg19: chr9-21815589;