rs11625206

chr14-70727436-C-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_001284230.2(MAP3K9):c.*2944G>A variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.253 in 152,186 control chromosomes in the GnomAD database, including 6,203 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 0.25 (6203 hom., cov: 32)
  • Exomes 𝑓: 0.16 (0 hom.)
• Consequence: MAP3K9 NM_001284230.2 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.118

Genes affected

MAP3K9 (HGNC:6861): (mitogen-activated protein kinase kinase kinase 9) Enables protein serine/threonine kinase activity. Involved in protein autophosphorylation. [provided by Alliance of Genome Resources, Apr 2022]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.341 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
MAP3K9	NM_001284230.2	c.*2944G>A		3_prime_UTR_variant	12/12	ENST00000554752.7

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
MAP3K9	ENST00000554752.7	c.*2944G>A		3_prime_UTR_variant	12/12	1	NM_001284230.2	P4

Frequencies

GnomAD3 genomes AF: 0.253 AC: 38506 AN: 151992 Hom.: 6206 Cov.: 32

Gnomad AFR AF: 0.0825

Gnomad AMI AF: 0.195

Gnomad AMR AF: 0.299

Gnomad ASJ AF: 0.297

Gnomad EAS AF: 0.00654

Gnomad SAS AF: 0.201

Gnomad FIN AF: 0.407

Gnomad MID AF: 0.241

Gnomad NFE AF: 0.344

Gnomad OTH AF: 0.249

GnomAD4 exome AF: 0.158 AC: 12 AN: 76 Hom.: 0 Cov.: 0 AF XY: 0.179 AC XY: 10 AN XY: 56

Gnomad4 AFR exome AF: 0.250

Gnomad4 ASJ exome AF: 0.250

Gnomad4 EAS exome AF: 0.00

Gnomad4 FIN exome AF: 0.00

Gnomad4 NFE exome AF: 0.205

Gnomad4 OTH exome AF: 0.0833

GnomAD4 genome AF: 0.253 AC: 38505 AN: 152110 Hom.: 6203 Cov.: 32 AF XY: 0.255 AC XY: 18989 AN XY: 74360

Gnomad4 AFR AF: 0.0822

Gnomad4 AMR AF: 0.300

Gnomad4 ASJ AF: 0.297

Gnomad4 EAS AF: 0.00656

Gnomad4 SAS AF: 0.202

Gnomad4 FIN AF: 0.407

Gnomad4 NFE AF: 0.344

Gnomad4 OTH AF: 0.247

Alfa AF: 0.313 Hom.: 4335

Bravo AF: 0.240

Asia WGS AF: 0.0980 AC: 341 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
Cadd	Benign	3.9
Dann	Benign	0.54

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs11625206; hg19: chr14-71194153;