rs6749643

Variant names:

• chr2-189970747-G-A
• rs6749643
• XM_047446008.1:c.-518+73184G>A

Variant summary

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

The ENST00000478197.1(C2orf88):​n.219+90920G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.238 in 152,120 control chromosomes in the GnomAD database, including 5,135 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 0.24 (5135 hom., cov: 32)
• Consequence: C2orf88 ENST00000478197.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.192
• 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=-1.01).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.401 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+90920G>A		intron	N/A
	C2orf88	ENST00000495546.1	TSL:4	n.201+90920G>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.238 AC: 36125 AN: 152002 Hom.: 5126 Cov.: 32

Gnomad AFR AF: 0.406

Gnomad AMI AF: 0.0899

Gnomad AMR AF: 0.166

Gnomad ASJ AF: 0.231

Gnomad EAS AF: 0.0998

Gnomad SAS AF: 0.161

Gnomad FIN AF: 0.157

Gnomad MID AF: 0.294

Gnomad NFE AF: 0.182

Gnomad OTH AF: 0.237

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

GnomAD4 genome AF: 0.238 AC: 36171 AN: 152120 Hom.: 5135 Cov.: 32 AF XY: 0.233 AC XY: 17317 AN XY: 74390

African (AFR) AF: 0.406 AC: 16815 AN: 41450

American (AMR) AF: 0.166 AC: 2532 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.231 AC: 802 AN: 3472

East Asian (EAS) AF: 0.0995 AC: 516 AN: 5186

South Asian (SAS) AF: 0.161 AC: 774 AN: 4818

European-Finnish (FIN) AF: 0.157 AC: 1664 AN: 10572

Middle Eastern (MID) AF: 0.299 AC: 88 AN: 294

European-Non Finnish (NFE) AF: 0.182 AC: 12393 AN: 68012

Other (OTH) AF: 0.239 AC: 505 AN: 2114

Alfa AF: 0.202 Hom.: 11240

Bravo AF: 0.247

Asia WGS AF: 0.178 AC: 618 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	1.4
DANN	Benign	0.31
PhyloP100		0.19

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: rs6749643;

hg19: chr2-190835473;