18-5195888-T-C

Variant names:

• chr18-5195888-T-C
• rs292283
• NM_001145194.2:c.16+1150A>G

Variant summary

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

The NM_001145194.2(AKAIN1):​c.16+1150A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0653 in 152,170 control chromosomes in the GnomAD database, including 379 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 0.065 (379 hom., cov: 32)
• Consequence: AKAIN1 NM_001145194.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.49
• Publications: 1 publications found

Genes affected

AKAIN1 (HGNC:28285): (A-kinase anchor inhibitor 1) Enables protein kinase A binding activity. Involved in protein localization. Predicted to be located in cytosol. [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=-0.82).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.0718 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001145194.2. 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
	AKAIN1	NM_001145194.2	MANE Select	c.16+1150A>G		intron	N/A	NP_001138666.1	P0CW23
	AKAIN1	NM_001330553.2		c.37+1564A>G		intron	N/A	NP_001317482.1	J3KS16

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	AKAIN1	ENST00000434239.4	TSL:2 MANE Select	c.16+1150A>G		intron	N/A	ENSP00000399075.3	P0CW23
	AKAIN1	ENST00000580650.1	TSL:3	c.37+1564A>G		intron	N/A	ENSP00000462259.1	J3KS16

Frequencies

GnomAD3 genomes AF: 0.0653 AC: 9923 AN: 152052 Hom.: 379 Cov.: 32

Gnomad AFR AF: 0.0739

Gnomad AMI AF: 0.0406

Gnomad AMR AF: 0.0370

Gnomad ASJ AF: 0.0435

Gnomad EAS AF: 0.0247

Gnomad SAS AF: 0.0725

Gnomad FIN AF: 0.105

Gnomad MID AF: 0.0538

Gnomad NFE AF: 0.0643

Gnomad OTH AF: 0.0623

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

GnomAD4 genome AF: 0.0653 AC: 9937 AN: 152170 Hom.: 379 Cov.: 32 AF XY: 0.0664 AC XY: 4942 AN XY: 74400

African (AFR) AF: 0.0740 AC: 3071 AN: 41516

American (AMR) AF: 0.0369 AC: 565 AN: 15296

Ashkenazi Jewish (ASJ) AF: 0.0435 AC: 151 AN: 3472

East Asian (EAS) AF: 0.0248 AC: 128 AN: 5160

South Asian (SAS) AF: 0.0734 AC: 354 AN: 4822

European-Finnish (FIN) AF: 0.105 AC: 1114 AN: 10600

Middle Eastern (MID) AF: 0.0578 AC: 17 AN: 294

European-Non Finnish (NFE) AF: 0.0643 AC: 4370 AN: 67988

Other (OTH) AF: 0.0616 AC: 130 AN: 2110

Alfa AF: 0.0617 Hom.: 470

Bravo AF: 0.0594

Asia WGS AF: 0.0600 AC: 207 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	9.0
DANN	Benign	0.71
PhyloP100		1.5
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: rs292283; hg19: chr18-5195887;