rs16832404

Variant names:

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

Your query was ambiguous. Multiple possible variants found:

• chr2-190188403-T-C
• chr2-190188403-T-G

Variant summary

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

The NM_001042519.2(AKAP19):​c.-165+7294T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.118 in 152,272 control chromosomes in the GnomAD database, including 1,171 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 0.12 (1171 hom., 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: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.64).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.253 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
AKAP19	NM_001042519.2	c.-165+7294T>C		intron_variant	Intron 1 of 1	ENST00000340623.4	NP_001035984.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
C2orf88	ENST00000340623.4	c.-165+7294T>C		intron_variant	Intron 1 of 1	1	NM_001042519.2	ENSP00000345107.4

Frequencies

GnomAD3 genomes AF: 0.118 AC: 18012 AN: 152154 Hom.: 1171 Cov.: 32

Gnomad AFR AF: 0.137

Gnomad AMI AF: 0.0395

Gnomad AMR AF: 0.152

Gnomad ASJ AF: 0.0455

Gnomad EAS AF: 0.265

Gnomad SAS AF: 0.0815

Gnomad FIN AF: 0.0976

Gnomad MID AF: 0.104

Gnomad NFE AF: 0.0994

Gnomad OTH AF: 0.113

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

GnomAD4 genome AF: 0.118 AC: 18031 AN: 152272 Hom.: 1171 Cov.: 32 AF XY: 0.118 AC XY: 8805 AN XY: 74448

African (AFR) AF: 0.136 AC: 5669 AN: 41550

American (AMR) AF: 0.152 AC: 2328 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.0455 AC: 158 AN: 3472

East Asian (EAS) AF: 0.265 AC: 1372 AN: 5180

South Asian (SAS) AF: 0.0816 AC: 394 AN: 4830

European-Finnish (FIN) AF: 0.0976 AC: 1036 AN: 10612

Middle Eastern (MID) AF: 0.0918 AC: 27 AN: 294

European-Non Finnish (NFE) AF: 0.0994 AC: 6759 AN: 68016

Other (OTH) AF: 0.119 AC: 252 AN: 2114

Alfa AF: 0.105 Hom.: 3602

Bravo AF: 0.123

Asia WGS AF: 0.188 AC: 651 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.64
CADD	Benign	15
DANN	Benign	0.95
PhyloP100		0.96
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: rs16832404; hg19: chr2-191053129;