NM_025052.5:c.575-1699A>G

Variant names:

• chr2-134993279-T-C
• rs2322254
• NM_025052.5:c.575-1699A>G

Variant summary

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

The NM_025052.5(MAP3K19):​c.575-1699A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.295 in 152,068 control chromosomes in the GnomAD database, including 7,411 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 (7411 hom., cov: 32)
• Consequence: MAP3K19 NM_025052.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.30
• Publications: 4 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: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.538 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_025052.5. 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
	MAP3K19	NM_025052.5	MANE Select	c.575-1699A>G		intron	N/A	NP_079328.3
	MAP3K19	NM_001400438.1		c.575-1699A>G		intron	N/A	NP_001387367.1
	MAP3K19	NM_001018044.3		c.236-1699A>G		intron	N/A	NP_001018054.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	MAP3K19	ENST00000392915.7	TSL:5 MANE Select	c.575-1699A>G		intron	N/A	ENSP00000376647.2
	MAP3K19	ENST00000375845.8	TSL:1	c.575-1699A>G		intron	N/A	ENSP00000365005.3
	MAP3K19	ENST00000358371.9	TSL:1	c.236-1699A>G		intron	N/A	ENSP00000351140.4

Frequencies

GnomAD3 genomes AF: 0.295 AC: 44821 AN: 151948 Hom.: 7391 Cov.: 32

Gnomad AFR AF: 0.368

Gnomad AMI AF: 0.309

Gnomad AMR AF: 0.294

Gnomad ASJ AF: 0.464

Gnomad EAS AF: 0.554

Gnomad SAS AF: 0.387

Gnomad FIN AF: 0.253

Gnomad MID AF: 0.618

Gnomad NFE AF: 0.220

Gnomad OTH AF: 0.329

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

GnomAD4 genome AF: 0.295 AC: 44889 AN: 152068 Hom.: 7411 Cov.: 32 AF XY: 0.303 AC XY: 22537 AN XY: 74328

African (AFR) AF: 0.368 AC: 15280 AN: 41480

American (AMR) AF: 0.294 AC: 4484 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.464 AC: 1610 AN: 3472

East Asian (EAS) AF: 0.555 AC: 2867 AN: 5166

South Asian (SAS) AF: 0.385 AC: 1852 AN: 4814

European-Finnish (FIN) AF: 0.253 AC: 2676 AN: 10572

Middle Eastern (MID) AF: 0.619 AC: 182 AN: 294

European-Non Finnish (NFE) AF: 0.220 AC: 14957 AN: 67976

Other (OTH) AF: 0.331 AC: 699 AN: 2110

Alfa AF: 0.272 Hom.: 810

Bravo AF: 0.301

Asia WGS AF: 0.458 AC: 1590 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.97
DANN	Benign	0.43
PhyloP100		-1.3
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: rs2322254; hg19: chr2-135750849;