chr9-125551165-A-C

Variant names:

• chr9-125551165-A-C
• rs536861
• NM_001006617.3:c.849-7997T>G

Variant summary

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

The NM_001006617.3(MAPKAP1):​c.849-7997T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.516 in 151,992 control chromosomes in the GnomAD database, including 20,967 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 0.52 (20967 hom., cov: 31)
• Consequence: MAPKAP1 NM_001006617.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.831
• Publications: 9 publications found

Genes affected

MAPKAP1 (HGNC:18752): (MAPK associated protein 1) This gene encodes a protein that is highly similar to the yeast SIN1 protein, a stress-activated protein kinase. Alternatively spliced transcript variants encoding distinct isoforms have been described. Alternate polyadenylation sites as well as alternate 3' UTRs have been identified for transcripts of this gene. [provided by RefSeq, Jul 2008]

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.646 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001006617.3. 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
	MAPKAP1	NM_001006617.3	MANE Select	c.849-7997T>G		intron	N/A	NP_001006618.1
	MAPKAP1	NM_024117.4		c.849-7997T>G		intron	N/A	NP_077022.1
	MAPKAP1	NM_001006619.2		c.849-7997T>G		intron	N/A	NP_001006620.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	MAPKAP1	ENST00000265960.8	TSL:1 MANE Select	c.849-7997T>G		intron	N/A	ENSP00000265960.3
	MAPKAP1	ENST00000350766.7	TSL:1	c.849-7997T>G		intron	N/A	ENSP00000265961.5
	MAPKAP1	ENST00000373511.6	TSL:1	c.849-7997T>G		intron	N/A	ENSP00000362610.2

Frequencies

GnomAD3 genomes AF: 0.516 AC: 78397 AN: 151872 Hom.: 20954 Cov.: 31

Gnomad AFR AF: 0.361

Gnomad AMI AF: 0.525

Gnomad AMR AF: 0.554

Gnomad ASJ AF: 0.596

Gnomad EAS AF: 0.664

Gnomad SAS AF: 0.627

Gnomad FIN AF: 0.526

Gnomad MID AF: 0.522

Gnomad NFE AF: 0.577

Gnomad OTH AF: 0.527

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

GnomAD4 genome AF: 0.516 AC: 78438 AN: 151992 Hom.: 20967 Cov.: 31 AF XY: 0.519 AC XY: 38525 AN XY: 74294

African (AFR) AF: 0.360 AC: 14944 AN: 41462

American (AMR) AF: 0.555 AC: 8482 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.596 AC: 2069 AN: 3470

East Asian (EAS) AF: 0.664 AC: 3426 AN: 5156

South Asian (SAS) AF: 0.629 AC: 3028 AN: 4816

European-Finnish (FIN) AF: 0.526 AC: 5551 AN: 10544

Middle Eastern (MID) AF: 0.507 AC: 148 AN: 292

European-Non Finnish (NFE) AF: 0.577 AC: 39193 AN: 67934

Other (OTH) AF: 0.529 AC: 1118 AN: 2114

Alfa AF: 0.441 Hom.: 1675

Bravo AF: 0.508

Asia WGS AF: 0.617 AC: 2144 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	9.3
DANN	Benign	0.70
PhyloP100		0.83
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: rs536861; hg19: chr9-128313444;