21-29086433-T-C

Variant summary

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

The ENST00000341618.8(MAP3K7CL):​c.57+516T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.176 in 152,090 control chromosomes in the GnomAD database, including 2,648 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 0.18 ( 2648 hom., cov: 32)

Consequence

MAP3K7CL
ENST00000341618.8 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.0540
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=-0.83).
BA1
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.266 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE Protein UniProt
MAP3K7CLNM_001286617.2 linkuse as main transcriptc.-482+516T>C intron_variant NP_001273546.1
MAP3K7CLNM_001286618.2 linkuse as main transcriptc.-353+516T>C intron_variant NP_001273547.1
MAP3K7CLNM_001286622.2 linkuse as main transcriptc.-406+516T>C intron_variant NP_001273551.1

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Protein Appris UniProt
MAP3K7CLENST00000341618.8 linkuse as main transcriptc.57+516T>C intron_variant 1 ENSP00000343212 P57077-1
MAP3K7CLENST00000399947.6 linkuse as main transcriptc.57+516T>C intron_variant 1 ENSP00000382828 P57077-1
MAP3K7CLENST00000496779.5 linkuse as main transcriptn.505+516T>C intron_variant, non_coding_transcript_variant 1

Frequencies

GnomAD3 genomes
AF:
0.176
AC:
26738
AN:
151972
Hom.:
2645
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.270
Gnomad AMI
AF:
0.0429
Gnomad AMR
AF:
0.180
Gnomad ASJ
AF:
0.182
Gnomad EAS
AF:
0.146
Gnomad SAS
AF:
0.123
Gnomad FIN
AF:
0.0886
Gnomad MID
AF:
0.180
Gnomad NFE
AF:
0.139
Gnomad OTH
AF:
0.181
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.176
AC:
26758
AN:
152090
Hom.:
2648
Cov.:
32
AF XY:
0.171
AC XY:
12723
AN XY:
74362
show subpopulations
Gnomad4 AFR
AF:
0.270
Gnomad4 AMR
AF:
0.180
Gnomad4 ASJ
AF:
0.182
Gnomad4 EAS
AF:
0.146
Gnomad4 SAS
AF:
0.123
Gnomad4 FIN
AF:
0.0886
Gnomad4 NFE
AF:
0.139
Gnomad4 OTH
AF:
0.182
Alfa
AF:
0.143
Hom.:
3351
Bravo
AF:
0.187
Asia WGS
AF:
0.154
AC:
536
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.83
CADD
Benign
4.7
DANN
Benign
0.72

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: rs8133819; hg19: chr21-30458754; API