chr9-125464514-G-A

Variant names:

• chr9-125464514-G-A
• rs10513448
• NM_001006617.3:c.1345+3458C>T

Variant summary

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

The NM_001006617.3(MAPKAP1):​c.1345+3458C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.06 in 152,164 control chromosomes in the GnomAD database, including 814 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 0.060 (814 hom., cov: 33)
• Consequence: MAPKAP1 NM_001006617.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.91
• Publications: 1 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=-0.91).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.196 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.1345+3458C>T		intron	N/A	NP_001006618.1
	MAPKAP1	NM_024117.4		c.1237+3458C>T		intron	N/A	NP_077022.1
	MAPKAP1	NM_001006619.2		c.1204+3458C>T		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.1345+3458C>T		intron	N/A	ENSP00000265960.3
	MAPKAP1	ENST00000350766.7	TSL:1	c.1237+3458C>T		intron	N/A	ENSP00000265961.5
	MAPKAP1	ENST00000373511.6	TSL:1	c.1204+3458C>T		intron	N/A	ENSP00000362610.2

Frequencies

GnomAD3 genomes AF: 0.0599 AC: 9113 AN: 152048 Hom.: 814 Cov.: 33

Gnomad AFR AF: 0.200

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0318

Gnomad ASJ AF: 0.0110

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.000622

Gnomad FIN AF: 0.00

Gnomad MID AF: 0.0475

Gnomad NFE AF: 0.00304

Gnomad OTH AF: 0.0540

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

GnomAD4 genome AF: 0.0600 AC: 9125 AN: 152164 Hom.: 814 Cov.: 33 AF XY: 0.0577 AC XY: 4296 AN XY: 74400

African (AFR) AF: 0.199 AC: 8266 AN: 41482

American (AMR) AF: 0.0317 AC: 485 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.0110 AC: 38 AN: 3466

East Asian (EAS) AF: 0.00 AC: 0 AN: 5180

South Asian (SAS) AF: 0.000207 AC: 1 AN: 4820

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 10602

Middle Eastern (MID) AF: 0.0510 AC: 15 AN: 294

European-Non Finnish (NFE) AF: 0.00304 AC: 207 AN: 68010

Other (OTH) AF: 0.0535 AC: 113 AN: 2114

Alfa AF: 0.0571 Hom.: 102

Bravo AF: 0.0697

Asia WGS AF: 0.0120 AC: 41 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.079
DANN	Benign	0.38
PhyloP100		-1.9
Mutation Taster		=100/0	polymorphism (auto)

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.010		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: rs10513448; hg19: chr9-128226793;