9-21815590-T-TAAA

Variant summary

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

The NM_002451.4(MTAP):c.120+83_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 0.79 (45740 hom., cov: 0)
  • Exomes 𝑓: 0.46 (6803 hom.)
  • Failed GnomAD Quality Control
• 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-TAAA is Benign according to our data. Variant chr9-21815590-T-TAAA is described in ClinVar as [Benign]. Clinvar id is 1229885.Status of the report is criteria_provided_single_submitter, 1 stars.
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.851 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
MTAP	NM_002451.4	c.120+83_120+85dup		intron_variant		ENST00000644715.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
MTAP	ENST00000644715.2	c.120+83_120+85dup		intron_variant			NM_002451.4	P1

Frequencies

GnomAD3 genomes AF: 0.786 AC: 114935 AN: 146210 Hom.: 45733 Cov.: 0

Gnomad AFR AF: 0.662

Gnomad AMI AF: 0.636

Gnomad AMR AF: 0.792

Gnomad ASJ AF: 0.804

Gnomad EAS AF: 0.725

Gnomad SAS AF: 0.826

Gnomad FIN AF: 0.823

Gnomad MID AF: 0.765

Gnomad NFE AF: 0.856

Gnomad OTH AF: 0.797

GnomAD3 exomes AF: 0.419 AC: 35861 AN: 85622 Hom.: 619 AF XY: 0.417 AC XY: 19493 AN XY: 46708

Gnomad AFR exome AF: 0.355

Gnomad AMR exome AF: 0.392

Gnomad ASJ exome AF: 0.405

Gnomad EAS exome AF: 0.393

Gnomad SAS exome AF: 0.406

Gnomad FIN exome AF: 0.461

Gnomad NFE exome AF: 0.428

Gnomad OTH exome AF: 0.422

GnomAD4 exome Data not reliable, filtered out with message: InbreedingCoeff AF: 0.456 AC: 276824 AN: 606932 Hom.: 6803 Cov.: 12 AF XY: 0.456 AC XY: 147286 AN XY: 323116

Gnomad4 AFR exome AF: 0.389

Gnomad4 AMR exome AF: 0.403

Gnomad4 ASJ exome AF: 0.438

Gnomad4 EAS exome AF: 0.424

Gnomad4 SAS exome AF: 0.443

Gnomad4 FIN exome AF: 0.461

Gnomad4 NFE exome AF: 0.466

Gnomad4 OTH exome AF: 0.445

GnomAD4 genome AF: 0.786 AC: 114967 AN: 146270 Hom.: 45740 Cov.: 0 AF XY: 0.786 AC XY: 55711 AN XY: 70850

Gnomad4 AFR AF: 0.662

Gnomad4 AMR AF: 0.792

Gnomad4 ASJ AF: 0.804

Gnomad4 EAS AF: 0.725

Gnomad4 SAS AF: 0.826

Gnomad4 FIN AF: 0.823

Gnomad4 NFE AF: 0.856

Gnomad4 OTH AF: 0.798

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

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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;