rs1454301

Variant names:

• chr2-189945336-A-C
• rs1454301
• XM_047446008.1:c.-518+47773A>C

Variant summary

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

The ENST00000478197.1(C2orf88):​n.219+65509A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.264 in 152,044 control chromosomes in the GnomAD database, including 6,435 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 0.26 (6435 hom., cov: 32)
• Consequence: C2orf88 ENST00000478197.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.365
• Publications: 5 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=-0.93).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.454 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000478197.1. 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
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	C2orf88	ENST00000478197.1	TSL:4	n.219+65509A>C		intron	N/A
	C2orf88	ENST00000495546.1	TSL:4	n.201+65509A>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.264 AC: 40081 AN: 151926 Hom.: 6424 Cov.: 32

Gnomad AFR AF: 0.459

Gnomad AMI AF: 0.0899

Gnomad AMR AF: 0.209

Gnomad ASJ AF: 0.242

Gnomad EAS AF: 0.253

Gnomad SAS AF: 0.171

Gnomad FIN AF: 0.159

Gnomad MID AF: 0.304

Gnomad NFE AF: 0.184

Gnomad OTH AF: 0.258

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

GnomAD4 genome AF: 0.264 AC: 40145 AN: 152044 Hom.: 6435 Cov.: 32 AF XY: 0.259 AC XY: 19283 AN XY: 74348

African (AFR) AF: 0.460 AC: 19035 AN: 41424

American (AMR) AF: 0.210 AC: 3205 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.242 AC: 839 AN: 3468

East Asian (EAS) AF: 0.253 AC: 1310 AN: 5178

South Asian (SAS) AF: 0.170 AC: 822 AN: 4824

European-Finnish (FIN) AF: 0.159 AC: 1680 AN: 10584

Middle Eastern (MID) AF: 0.310 AC: 91 AN: 294

European-Non Finnish (NFE) AF: 0.184 AC: 12533 AN: 67980

Other (OTH) AF: 0.260 AC: 548 AN: 2108

Alfa AF: 0.208 Hom.: 1963

Bravo AF: 0.281

Asia WGS AF: 0.229 AC: 797 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	1.9
DANN	Benign	0.66
PhyloP100		0.36

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs1454301;

hg19: chr2-190810062;