2-190188403-T-G

Variant names:

• chr2-190188403-T-G
• rs16832404
• NM_001042519.2:c.-165+7294T>G

Variant summary

Our verdict is Likely benign. The variant received -2 ACMG points: 2P and 4B. PM2 BP4_Strong

The NM_001042519.2(AKAP19):​c.-165+7294T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. 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: not found (cov: 32)
• Consequence: AKAP19 NM_001042519.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.957
• Publications: 6 publications found

Genes affected

AKAP19 (HGNC:28191): (chromosome 2 open reading frame 88) Predicted to enable protein kinase A regulatory subunit binding activity. Predicted to be located in plasma membrane. [provided by Alliance of Genome Resources, Apr 2022]

ACMG classification

Our verdict: Likely_benign. The variant received -2 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.62).

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001042519.2. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	AKAP19	NM_001042519.2	MANE Select	c.-165+7294T>G		intron	N/A	NP_001035984.1	Q9BSF0
	AKAP19	NM_001042520.2		c.-164-11294T>G		intron	N/A	NP_001035985.1	Q9BSF0
	AKAP19	NM_001042521.2		c.-164-11294T>G		intron	N/A	NP_001035986.1	Q9BSF0

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	C2orf88	ENST00000340623.4	TSL:1 MANE Select	c.-165+7294T>G		intron	N/A	ENSP00000345107.4	Q9BSF0
	C2orf88	ENST00000443551.2	TSL:1	c.-165+7275T>G		intron	N/A	ENSP00000405225.2	Q9BSF0
	C2orf88	ENST00000396974.2	TSL:2	c.-164-11294T>G		intron	N/A	ENSP00000380172.2	Q9BSF0

Frequencies

GnomAD3 genomes Cov.: 32

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

GnomAD4 genome Cov.: 32

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.62
CADD	Benign	15
DANN	Benign	0.94
PhyloP100		0.96

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: rs16832404; hg19: chr2-191053129;