rs10986769

Positions:

• chr9-125460061-A-G
• chr9-125460061-A-T

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_Moderate BA1

The NM_001006617.3(MAPKAP1):​c.1345+7911T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0201 in 152,218 control chromosomes in the GnomAD database, including 167 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 0.020 (167 hom., cov: 32)
• Consequence: MAPKAP1 NM_001006617.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.02

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

Verdict is Benign. Variant got -10 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.36).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.132 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
MAPKAP1	NM_001006617.3	c.1345+7911T>C		intron_variant		ENST00000265960.8	NP_001006618.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
MAPKAP1	ENST00000265960.8	c.1345+7911T>C		intron_variant		1	NM_001006617.3	ENSP00000265960.3

Frequencies

GnomAD3 genomes AF: 0.0201 AC: 3058 AN: 152100 Hom.: 167 Cov.: 32

Gnomad AFR AF: 0.00283

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0914

Gnomad ASJ AF: 0.0138

Gnomad EAS AF: 0.141

Gnomad SAS AF: 0.0189

Gnomad FIN AF: 0.0504

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.00163

Gnomad OTH AF: 0.0153

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

GnomAD4 genome AF: 0.0201 AC: 3057 AN: 152218 Hom.: 167 Cov.: 32 AF XY: 0.0241 AC XY: 1796 AN XY: 74412

Gnomad4 AFR AF: 0.00282

Gnomad4 AMR AF: 0.0916

Gnomad4 ASJ AF: 0.0138

Gnomad4 EAS AF: 0.140

Gnomad4 SAS AF: 0.0183

Gnomad4 FIN AF: 0.0504

Gnomad4 NFE AF: 0.00165

Gnomad4 OTH AF: 0.0147

Alfa AF: 0.0163 Hom.: 21

Bravo AF: 0.0242

Asia WGS AF: 0.0800 AC: 278 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.36
CADD	Benign	18
DANN	Benign	0.87

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

Publications

LitVar

Other links and lift over

dbSNP: rs10986769; hg19: chr9-128222340;