7-82590109-C-G

Variant names:

• chr7-82590109-C-G
• rs1981576
• ENST00000320415.6:n.583G>C

Variant summary

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

The ENST00000320415.6(MTHFD2P5):​n.583G>C variant causes a non coding transcript exon 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: 32)
  • Exomes 𝑓: 0.0 (0 hom.)
  • Failed GnomAD Quality Control
• Consequence: MTHFD2P5 ENST00000320415.6 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.64
• Publications: 2 publications found

Genes affected

MTHFD2P5 (HGNC:48863): (methylenetetrahydrofolate dehydrogenase (NADP+ dependent) 2, methenyltetrahydrofolate cyclohydrolase pseudogene 5)

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=-0.68).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
MTHFD2P5		n.82590109C>G		intragenic_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
MTHFD2P5	ENST00000320415.6	n.583G>C		non_coding_transcript_exon_variant	Exon 1 of 1	6

Frequencies

GnomAD3 genomes Cov.: 32

GnomAD4 exome Data not reliable, filtered out with message: AC0;AS_VQSR AF: 0.00 AC: 0 AN: 396672 Hom.: 0 Cov.: 2 AF XY: 0.00 AC XY: 0 AN XY: 223482

African (AFR) AF: 0.00 AC: 0 AN: 11198

American (AMR) AF: 0.00 AC: 0 AN: 35350

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 11694

East Asian (EAS) AF: 0.00 AC: 0 AN: 16150

South Asian (SAS) AF: 0.00 AC: 0 AN: 63754

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 31908

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 1302

European-Non Finnish (NFE) AF: 0.00 AC: 0 AN: 206856

Other (OTH) AF: 0.00 AC: 0 AN: 18460

GnomAD4 genome Cov.: 32

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.68
CADD	Benign	0.65
DANN	Benign	0.46
PhyloP100		-2.6

Splicing

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

Other links and lift over

dbSNP: rs1981576; hg19: chr7-82219425;