rs536861

chr9-125551165-A-Cchr9-125551165-A-T

Variant summary

Our verdict is Benign. Variant got -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

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 -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
MAPKAP1	NM_001006617.3	c.849-7997T>G		intron_variant		ENST00000265960.8

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
MAPKAP1	ENST00000265960.8	c.849-7997T>G		intron_variant		1	NM_001006617.3	P1

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

Gnomad4 AFR AF: 0.360

Gnomad4 AMR AF: 0.555

Gnomad4 ASJ AF: 0.596

Gnomad4 EAS AF: 0.664

Gnomad4 SAS AF: 0.629

Gnomad4 FIN AF: 0.526

Gnomad4 NFE AF: 0.577

Gnomad4 OTH AF: 0.529

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 v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
Cadd	Benign	9.3
Dann	Benign	0.70

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: rs536861; hg19: chr9-128313444;