Genetic Variant MAP3K7CL:c.*389A>G (chr21-29175281-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 NM_001286620.2(MAP3K7CL):c.*389A>G variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.591 in 154,984 control chromosomes in the GnomAD database, including 27,905 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 0.59 ( 27481 hom., cov: 32)

Exomes 𝑓: 0.53 ( 424 hom. )

Consequence

MAP3K7CL
NM_001286620.2 3_prime_UTR

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.577

Publications

11 publications found

Variant links:

Genes affected

MAP3K7CL (HGNC:16457): (MAP3K7 C-terminal like) Located in cytosol and nucleus. [provided by Alliance of Genome Resources, Apr 2022]

MAP3K7CL 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=-0.85).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.745 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001286620.2. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein
MAP3K7CL	NM_001286620.2	MANE Select	c.*389A>G	3_prime_UTR	Exon 5 of 5	NP_001273549.1
MAP3K7CL	NM_001286634.2		c.*389A>G	3_prime_UTR	Exon 8 of 8	NP_001273563.1
MAP3K7CL	NM_001371369.1		c.*389A>G	3_prime_UTR	Exon 9 of 9	NP_001358298.1

Ensembl Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein
MAP3K7CL	ENST00000399928.6	TSL:1 MANE Select	c.*389A>G	3_prime_UTR	Exon 5 of 5	ENSP00000382812.1
MAP3K7CL	ENST00000341618.8	TSL:1	c.*389A>G	3_prime_UTR	Exon 8 of 8	ENSP00000343212.4
MAP3K7CL	ENST00000399947.6	TSL:1	c.*389A>G	3_prime_UTR	Exon 9 of 9	ENSP00000382828.2

Frequencies

GnomAD3 genomes

AF:

0.592

AC:

89896

AN:

151904

Hom.:

27443

Cov.:

show subpopulations

Gnomad AFR

AF:

0.752

Gnomad AMI

AF:

0.701

Gnomad AMR

AF:

0.538

Gnomad ASJ

AF:

0.587

Gnomad EAS

AF:

0.400

Gnomad SAS

AF:

0.617

Gnomad FIN

AF:

0.542

Gnomad MID

AF:

0.548

Gnomad NFE

AF:

0.527

Gnomad OTH

AF:

0.556

GnomAD4 exome

AF:

0.530

AC:

1570

AN:

2960

Hom.:

424

Cov.:

AF XY:

0.529

AC XY:

810

AN XY:

1532

show subpopulations

African (AFR)

AF:

0.807

AC:

AN:

114

American (AMR)

AF:

0.484

AC:

AN:

124

Ashkenazi Jewish (ASJ)

AF:

0.579

AC:

AN:

114

East Asian (EAS)

AF:

0.333

AC:

AN:

South Asian (SAS)

AF:

0.678

AC:

AN:

European-Finnish (FIN)

AF:

0.500

AC:

AN:

Middle Eastern (MID)

AF:

0.375

AC:

AN:

European-Non Finnish (NFE)

AF:

0.518

AC:

1118

AN:

2160

Other (OTH)

AF:

0.546

AC:

107

AN:

196

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.506

Heterozygous variant carriers

118

148

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

100

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

GnomAD4 genome

AF:

0.592

AC:

89987

AN:

152024

Hom.:

27481

Cov.:

AF XY:

0.592

AC XY:

43981

AN XY:

74308

show subpopulations

African (AFR)

AF:

0.752

AC:

31207

AN:

41476

American (AMR)

AF:

0.537

AC:

8203

AN:

15272

Ashkenazi Jewish (ASJ)

AF:

0.587

AC:

2034

AN:

3468

East Asian (EAS)

AF:

0.399

AC:

2063

AN:

5174

South Asian (SAS)

AF:

0.616

AC:

2966

AN:

4812

European-Finnish (FIN)

AF:

0.542

AC:

5715

AN:

10542

Middle Eastern (MID)

AF:

0.561

AC:

165

AN:

294

European-Non Finnish (NFE)

AF:

0.527

AC:

35820

AN:

67962

Other (OTH)

AF:

0.556

AC:

1176

AN:

2114

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.503

Heterozygous variant carriers

1837

3674

5511

7348

9185

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

746

1492

2238

2984

3730

<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:

0.553

Hom.:

19069

Bravo

AF:

0.597

Asia WGS

AF:

0.529

AC:

1838

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.85

CADD

Benign

4.8

(source)

DANN

Benign

0.33

PhyloP100

0.58

Mutation Taster

=100/0

polymorphism (auto)

(source)

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

Publications

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Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Variant Effect in Transcripts

RefSeq Transcripts

Ensembl Transcripts

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over