rs2251517

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_001286620.2(MAP3K7CL):​c.133-311T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.426 in 151,942 control chromosomes in the GnomAD database, including 14,149 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 0.43 ( 14149 hom., cov: 31)

Consequence

MAP3K7CL
NM_001286620.2 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.107
Variant links:
Genes affected
MAP3K7CL (HGNC:16457): (MAP3K7 C-terminal like) Located in cytosol and nucleus. [provided by Alliance of Genome Resources, Apr 2022]

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.9).
BA1
GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.479 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
MAP3K7CLNM_001286620.2 linkuse as main transcriptc.133-311T>G intron_variant ENST00000399928.6

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
MAP3K7CLENST00000399928.6 linkuse as main transcriptc.133-311T>G intron_variant 1 NM_001286620.2 P1P57077-4

Frequencies

GnomAD3 genomes
AF:
0.425
AC:
64596
AN:
151824
Hom.:
14132
Cov.:
31
show subpopulations
Gnomad AFR
AF:
0.351
Gnomad AMI
AF:
0.631
Gnomad AMR
AF:
0.384
Gnomad ASJ
AF:
0.459
Gnomad EAS
AF:
0.255
Gnomad SAS
AF:
0.496
Gnomad FIN
AF:
0.518
Gnomad MID
AF:
0.373
Gnomad NFE
AF:
0.470
Gnomad OTH
AF:
0.422
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.426
AC:
64652
AN:
151942
Hom.:
14149
Cov.:
31
AF XY:
0.427
AC XY:
31736
AN XY:
74256
show subpopulations
Gnomad4 AFR
AF:
0.351
Gnomad4 AMR
AF:
0.384
Gnomad4 ASJ
AF:
0.459
Gnomad4 EAS
AF:
0.254
Gnomad4 SAS
AF:
0.496
Gnomad4 FIN
AF:
0.518
Gnomad4 NFE
AF:
0.470
Gnomad4 OTH
AF:
0.421
Alfa
AF:
0.444
Hom.:
3397
Bravo
AF:
0.412
Asia WGS
AF:
0.380
AC:
1318
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.90
CADD
Benign
1.8
DANN
Benign
0.38

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

LitVar

Below is the list of publications found by LitVar. It may be empty.

Other links and lift over

dbSNP: rs2251517; hg19: chr21-30531951; API