Genetic Variant MAP4K3-DT:n.73-30205G>T (chr2-39616057-G-T) – ACMG Classification: Benign (-12 pts)

Variant summary

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

The ENST00000415640.1(MAP4K3-DT):n.73-30205G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.352 in 152,034 control chromosomes in the GnomAD database, including 9,551 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 0.35 ( 9551 hom., cov: 32)

Consequence

MAP4K3-DT
ENST00000415640.1 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.0260

Publications

8 publications found

Variant links:

Genes affected

MAP4K3-DT (HGNC:54056): (MAP4K3 divergent transcript)

MAP4K3-DT links:

Genome browser will be placed here

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=-0.76).

BA1

GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.42 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
MAP4K3-DT	ENST00000415640.1 link	n.73-30205G>T	intron_variant	Intron 1 of 2	3
MAP4K3-DT	ENST00000446698.7 link	n.531-8042G>T	intron_variant	Intron 5 of 5	5
MAP4K3-DT	ENST00000670934.1 link	n.522-13938G>T	intron_variant	Intron 5 of 5

Frequencies

GnomAD3 genomes

AF:

0.352

AC:

53421

AN:

151916

Hom.:

9536

Cov.:

show subpopulations

Gnomad AFR

AF:

0.324

Gnomad AMI

AF:

0.392

Gnomad AMR

AF:

0.315

Gnomad ASJ

AF:

0.332

Gnomad EAS

AF:

0.372

Gnomad SAS

AF:

0.436

Gnomad FIN

AF:

0.376

Gnomad MID

AF:

0.449

Gnomad NFE

AF:

0.366

Gnomad OTH

AF:

0.354

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

GnomAD4 genome

AF:

0.352

AC:

53461

AN:

152034

Hom.:

9551

Cov.:

AF XY:

0.353

AC XY:

26239

AN XY:

74308

show subpopulations

African (AFR)

AF:

0.324

AC:

13415

AN:

41466

American (AMR)

AF:

0.315

AC:

4807

AN:

15262

Ashkenazi Jewish (ASJ)

AF:

0.332

AC:

1153

AN:

3468

East Asian (EAS)

AF:

0.371

AC:

1920

AN:

5174

South Asian (SAS)

AF:

0.435

AC:

2096

AN:

4814

European-Finnish (FIN)

AF:

0.376

AC:

3973

AN:

10570

Middle Eastern (MID)

AF:

0.459

AC:

135

AN:

294

European-Non Finnish (NFE)

AF:

0.366

AC:

24847

AN:

67964

Other (OTH)

AF:

0.359

AC:

758

AN:

2112

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.503

Heterozygous variant carriers

1791

3582

5372

7163

8954

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

536

1072

1608

2144

2680

<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:

0.304

Hom.:

2905

Bravo

AF:

0.346

Asia WGS

AF:

0.464

AC:

1612

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.76

CADD

Benign

7.9

(source)

DANN

Benign

0.76

PhyloP100

-0.026

Splicing

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

Publications

You must be logged in to view publications. This limit was set because tens of millions (!) of queries from AI bots are generated daily.

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