rs4954218

Variant names:

• chr2-135045855-G-A
• rs4954218
• NM_025052.5:c.-424+1330C>T

Your query was ambiguous. Multiple possible variants found:

• chr2-135045855-G-A
• chr2-135045855-G-C
• chr2-135045855-G-T

Variant summary

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

The NM_025052.5(MAP3K19):​c.-424+1330C>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: 33)
• Consequence: MAP3K19 NM_025052.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0840
• Publications: 39 publications found

Genes affected

MAP3K19 (HGNC:26249): (mitogen-activated protein kinase kinase kinase 19) Predicted to enable ATP binding activity; protein serine kinase activity; and protein serine/threonine kinase activity. Predicted to be involved in protein phosphorylation. [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=-0.85).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
MAP3K19	NM_025052.5	c.-424+1330C>T		intron_variant	Intron 1 of 12	ENST00000392915.7	NP_079328.3
MAP3K19	NM_001400438.1	c.-480+1330C>T		intron_variant	Intron 1 of 12		NP_001387367.1
MAP3K19	XM_017005004.3	c.-392+1330C>T		intron_variant	Intron 1 of 11		XP_016860493.1
MAP3K19	XM_017005005.3	c.-203+1330C>T		intron_variant	Intron 1 of 10		XP_016860494.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
MAP3K19	ENST00000392915.7	c.-424+1330C>T		intron_variant	Intron 1 of 12	5	NM_025052.5	ENSP00000376647.2

Frequencies

GnomAD3 genomes Cov.: 33

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

GnomAD4 genome Cov.: 33

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	0.73
DANN	Benign	0.89
PhyloP100		-0.084

Splicing

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

Other links and lift over

dbSNP: rs4954218; hg19: chr2-135803425;