Genetic Variant MTHFD2P1:n.84+3972T>C (chr3-95718045-A-G) – ACMG Classification: Benign (-12 pts)

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBA1

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

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -1.49

Publications

0 publications found

Variant links:

Genes affected

MTHFD2P1 (HGNC:):

MTHFD2P1 links:

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ACMG classification

Classification was made for transcript

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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank	TSL
MTHFD2P1	ENST00000463799.2 link	n.84+3972T>C	intron_variant	Intron 1 of 4	3
MTHFD2P1	ENST00000785187.1 link	n.87+3972T>C	intron_variant	Intron 1 of 2
MTHFD2P1	ENST00000785188.1 link	n.63+3972T>C	intron_variant	Intron 1 of 2

Frequencies

GnomAD3 genomes

AF:

0.448

AC:

67960

AN:

151832

Hom.:

16366

Cov.:

show subpopulations

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.:

AF XY:

0.449

AC XY:

33332

AN XY:

74252

show subpopulations

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

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.504

Heterozygous variant carriers

1788

3576

5363

7151

8939

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

634

1268

1902

2536

3170

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

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 v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.96

CADD

Benign

0.025

(source)

DANN

Benign

0.42

PhyloP100

-1.5

Splicing

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

Publications

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Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over