chr6-90545615-G-A

Variant names:

• chr6-90545615-G-A
• rs1145729
• NM_145331.3:c.1211-983C>T

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_145331.3(MAP3K7):​c.1211-983C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.3 in 151,960 control chromosomes in the GnomAD database, including 7,309 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 0.30 (7309 hom., cov: 31)
• Consequence: MAP3K7 NM_145331.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.529
• Publications: 4 publications found

Genes affected

MAP3K7 (HGNC:6859): (mitogen-activated protein kinase kinase kinase 7) The protein encoded by this gene is a member of the serine/threonine protein kinase family. This kinase mediates the signaling transduction induced by TGF beta and morphogenetic protein (BMP), and controls a variety of cell functions including transcription regulation and apoptosis. In response to IL-1, this protein forms a kinase complex including TRAF6, MAP3K7P1/TAB1 and MAP3K7P2/TAB2; this complex is required for the activation of nuclear factor kappa B. This kinase can also activate MAPK8/JNK, MAP2K4/MKK4, and thus plays a role in the cell response to environmental stresses. Four alternatively spliced transcript variants encoding distinct isoforms have been reported. [provided by RefSeq, Jul 2008]

MAP3K7 Gene-Disease associations (from GenCC):

• cardiospondylocarpofacial syndrome

  Inheritance: AD Classification: STRONG, SUPPORTIVE Submitted by: Ambry Genetics, Orphanet, Labcorp Genetics (formerly Invitae)
• frontometaphyseal dysplasia

  Inheritance: AD Classification: STRONG, SUPPORTIVE Submitted by: Orphanet, Illumina
• frontometaphyseal dysplasia 2

  Inheritance: AD Classification: STRONG Submitted by: Ambry Genetics, G2P, Labcorp Genetics (formerly Invitae)

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.359 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_145331.3. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	MAP3K7	NM_145331.3	MANE Select	c.1211-983C>T		intron	N/A	NP_663304.1
	MAP3K7	NM_003188.4		c.1210+1643C>T		intron	N/A	NP_003179.1
	MAP3K7	NM_145332.3		c.1211-983C>T		intron	N/A	NP_663305.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	MAP3K7	ENST00000369329.8	TSL:1 MANE Select	c.1211-983C>T		intron	N/A	ENSP00000358335.3
	MAP3K7	ENST00000369332.7	TSL:1	c.1210+1643C>T		intron	N/A	ENSP00000358338.3
	MAP3K7	ENST00000369325.7	TSL:1	c.1211-983C>T		intron	N/A	ENSP00000358331.3

Frequencies

GnomAD3 genomes AF: 0.301 AC: 45640 AN: 151842 Hom.: 7315 Cov.: 31

Gnomad AFR AF: 0.222

Gnomad AMI AF: 0.286

Gnomad AMR AF: 0.254

Gnomad ASJ AF: 0.315

Gnomad EAS AF: 0.116

Gnomad SAS AF: 0.227

Gnomad FIN AF: 0.390

Gnomad MID AF: 0.348

Gnomad NFE AF: 0.363

Gnomad OTH AF: 0.310

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

GnomAD4 genome AF: 0.300 AC: 45632 AN: 151960 Hom.: 7309 Cov.: 31 AF XY: 0.299 AC XY: 22243 AN XY: 74268

African (AFR) AF: 0.222 AC: 9196 AN: 41456

American (AMR) AF: 0.254 AC: 3879 AN: 15260

Ashkenazi Jewish (ASJ) AF: 0.315 AC: 1093 AN: 3468

East Asian (EAS) AF: 0.117 AC: 602 AN: 5158

South Asian (SAS) AF: 0.226 AC: 1090 AN: 4816

European-Finnish (FIN) AF: 0.390 AC: 4121 AN: 10558

Middle Eastern (MID) AF: 0.330 AC: 97 AN: 294

European-Non Finnish (NFE) AF: 0.363 AC: 24644 AN: 67940

Other (OTH) AF: 0.309 AC: 651 AN: 2104

Alfa AF: 0.335 Hom.: 1156

Bravo AF: 0.288

Asia WGS AF: 0.216 AC: 749 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	7.3
DANN	Benign	0.73
PhyloP100		0.53
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs1145729; hg19: chr6-91255334;