ENST00000463799.2:n.84+3972T>C

Variant names:

• chr3-95718045-A-G
• rs1533148
• ENST00000463799.2:n.84+3972T>C

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000463799.2(MTHFD2P1):​n.84+3972T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.448 in 151,950 control chromosomes in the GnomAD database, including 16,414 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 0.45 (16414 hom., cov: 31)
• Consequence: MTHFD2P1 ENST00000463799.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.49
• Publications: 0 publications found

Genes affected

MTHFD2P1 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.619 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000463799.2. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	MTHFD2P1	ENST00000463799.2	TSL:3	n.84+3972T>C		intron	N/A
	MTHFD2P1	ENST00000785187.1		n.87+3972T>C		intron	N/A
	MTHFD2P1	ENST00000785188.1		n.63+3972T>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.448 AC: 67960 AN: 151832 Hom.: 16366 Cov.: 31

Gnomad AFR AF: 0.625

Gnomad AMI AF: 0.341

Gnomad AMR AF: 0.300

Gnomad ASJ AF: 0.302

Gnomad EAS AF: 0.498

Gnomad SAS AF: 0.536

Gnomad FIN AF: 0.421

Gnomad MID AF: 0.354

Gnomad NFE AF: 0.377

Gnomad OTH AF: 0.406

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.448 AC: 68060 AN: 151950 Hom.: 16414 Cov.: 31 AF XY: 0.449 AC XY: 33332 AN XY: 74252

African (AFR) AF: 0.625 AC: 25908 AN: 41420

American (AMR) AF: 0.300 AC: 4575 AN: 15256

Ashkenazi Jewish (ASJ) AF: 0.302 AC: 1046 AN: 3468

East Asian (EAS) AF: 0.497 AC: 2561 AN: 5150

South Asian (SAS) AF: 0.538 AC: 2594 AN: 4818

European-Finnish (FIN) AF: 0.421 AC: 4452 AN: 10566

Middle Eastern (MID) AF: 0.344 AC: 101 AN: 294

European-Non Finnish (NFE) AF: 0.377 AC: 25650 AN: 67952

Other (OTH) AF: 0.408 AC: 863 AN: 2116

Alfa AF: 0.279 Hom.: 684

Bravo AF: 0.440

Asia WGS AF: 0.580 AC: 2012 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	0.025
DANN	Benign	0.42
PhyloP100		-1.5

Splicing

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

Other links and lift over

dbSNP: rs1533148; hg19: chr3-95436889;