rs17108533

Variant names:

• chr14-70783085-C-A
• rs17108533
• NM_001284230.2:c.820+17582G>T

Your query was ambiguous. Multiple possible variants found:

• chr14-70783085-C-A
• chr14-70783085-C-G
• chr14-70783085-C-T

Variant summary

Our verdict is Likely benign. The variant received -2 ACMG points: 2P and 4B. PM2 BP4_Strong

The NM_001284230.2(MAP3K9):​c.820+17582G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. 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: not found (cov: 32)
• Consequence: MAP3K9 NM_001284230.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0470
• Publications: 6 publications found

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

Our verdict: Likely_benign. The variant received -2 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001284230.2. 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
	MAP3K9	NM_001284230.2	MANE Select	c.820+17582G>T		intron	N/A	NP_001271159.1
	MAP3K9	NM_033141.4		c.820+17582G>T		intron	N/A	NP_149132.2
	MAP3K9	NM_001284231.1		c.-16+138G>T		intron	N/A	NP_001271160.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	MAP3K9	ENST00000554752.7	TSL:1 MANE Select	c.820+17582G>T		intron	N/A	ENSP00000451612.2
	MAP3K9	ENST00000555993.6	TSL:1	c.820+17582G>T		intron	N/A	ENSP00000451263.2
	MAP3K9	ENST00000553414.5	TSL:1	c.-99+138G>T		intron	N/A	ENSP00000451038.1

Frequencies

GnomAD3 genomes Cov.: 32

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

GnomAD4 genome Cov.: 32

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	2.3
DANN	Benign	0.18
PhyloP100		0.047
PromoterAI		-0.023	Neutral

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: rs17108533; hg19: chr14-71249802;