rs7864029

Variant names:

• chr9-21930148-G-A
• rs7864029
• ENST00000580900.5:c.814-860G>A

Your query was ambiguous. Multiple possible variants found:

• chr9-21930148-G-A
• chr9-21930148-G-C

Variant summary

Our verdict is Likely benign. The variant received -2 ACMG points: 2P and 4B. PM2 BP4_Strong

The ENST00000580900.5(MTAP):​c.814-860G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. 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: not found (cov: 33)
  • Exomes 𝑓: 0.0 (0 hom.)
  • Failed GnomAD Quality Control
• Consequence: MTAP ENST00000580900.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.671
• Publications: 3 publications found

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]

ERVFRD-3 (HGNC:49792): (endogenous retrovirus group FRD member 3)

ENSG00000264545 (HGNC:):

ACMG classification

Our verdict: Likely_benign. The variant received -2 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
MTAP	NM_001396044.1	c.814-860G>A		intron_variant	Intron 7 of 9		NP_001382973.1
MTAP	NM_001396041.1	c.814-860G>A		intron_variant	Intron 7 of 7		NP_001382970.1
MTAP	NM_001396045.1	c.691-860G>A		intron_variant	Intron 6 of 8		NP_001382974.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
MTAP	ENST00000580900.5	c.814-860G>A		intron_variant	Intron 7 of 7	1		ENSP00000463424.1
MTAP	ENST00000577563.1	c.148-860G>A		intron_variant	Intron 1 of 1	1		ENSP00000462082.1
ERVFRD-3	ENST00000578561.1	n.692G>A		non_coding_transcript_exon_variant	Exon 1 of 1	6

Frequencies

GnomAD3 genomes Cov.: 33

GnomAD4 exome Data not reliable, filtered out with message: AC0 AF: 0.00 AC: 0 AN: 250314 Hom.: 0 Cov.: 0 AF XY: 0.00 AC XY: 0 AN XY: 144008

African (AFR) AF: 0.00 AC: 0 AN: 7400

American (AMR) AF: 0.00 AC: 0 AN: 20058

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 6954

East Asian (EAS) AF: 0.00 AC: 0 AN: 10808

South Asian (SAS) AF: 0.00 AC: 0 AN: 43248

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 10730

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 2464

European-Non Finnish (NFE) AF: 0.00 AC: 0 AN: 136612

Other (OTH) AF: 0.00 AC: 0 AN: 12040

GnomAD4 genome Cov.: 33

Alfa AF: 0.00 Hom.: 409

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	0.64
DANN	Benign	0.89
PhyloP100		-0.67

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: rs7864029; hg19: chr9-21930147;